PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID 919450
Common NameARALYDRAFT_919450
Organism
Arabidopsis lyrata
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: 95465.6 Da    PI: 6.6331
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
919450genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B371.51.1e-22160261199
             EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEEE CS
      B3   1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvkvf 97 
             f+k+lt sd++++g +++ +++a+e+      + + + +++l+ +d++ ++W++++i+r++++r++l++GW+ Fv++++L +gD ++F   + +++el+v+v+
  919450 160 FCKTLTASDTSTHGGFSVLRRHADEClppldmSRQ-PPTQELVAKDLHANEWRFRHIFRGQPRRHLLQSGWSVFVSSKRLVAGDAFIFL--RGENGELRVGVR 259
             99*****************************7333.34459************************************************..449999*****9 PP

             -S CS
      B3  98 rk 99 
             r+
  919450 260 RA 261
             96 PP
2Auxin_resp118.84.3e-39286368183
  Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                 a+ha+st+++F+v+Y+Pr+s+seF+v+++++++++k+++s+GmRfkm+fe+e+++e+r++Gt+vg++d+d +rWp+SkWrsLk
      919450 286 AWHAISTGTMFTVYYKPRTSPSEFIVPFDQYMESVKNNYSIGMRFKMRFEGEEAPEQRFTGTIVGIEDSDITRWPKSKWRSLK 368
                 89*******************************************************************************96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.101.2E-40156275IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019363.14E-40157289IPR015300DNA-binding pseudobarrel domain
CDDcd100171.46E-20158260No hitNo description
SMARTSM010194.1E-22160262IPR003340B3 DNA binding domain
PfamPF023621.5E-20160261IPR003340B3 DNA binding domain
PROSITE profilePS5086311.42160262IPR003340B3 DNA binding domain
PfamPF065071.6E-36286368IPR010525Auxin response factor
PfamPF023092.2E-9720818IPR033389AUX/IAA domain
SuperFamilySSF542771.03E-11732810No hitNo description
PROSITE profilePS5174525.174733817IPR000270PB1 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:0005515Molecular Functionprotein binding
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 859 aa     Download sequence    Send to blast
MASSEVSMKG NRGGDNFSSS AFSDPKETRN GEGQKSNSSR PAAAERAVDP EAALYRELWH  60
ACAGPLVTVP RQDDRVFYFP QGHIEQVEAS TNQAAEQQMP LYDLPSKLLC RVINVDLKAE  120
ADTDEVYAQI TLLPEANQDE NAIEKEAPPP PPPRFQVHSF CKTLTASDTS THGGFSVLRR  180
HADECLPPLD MSRQPPTQEL VAKDLHANEW RFRHIFRGQP RRHLLQSGWS VFVSSKRLVA  240
GDAFIFLRGE NGELRVGVRR AMRQQGNVPS SVISSHSMHL GVLATAWHAI STGTMFTVYY  300
KPRTSPSEFI VPFDQYMESV KNNYSIGMRF KMRFEGEEAP EQRFTGTIVG IEDSDITRWP  360
KSKWRSLKVR WDETSSIPRP DRVSPWKIEP ALAPPALSPV PMPRPKRPRS NIAPSSPDSS  420
MLTREGTTKA NMDPLPASGL SRVLQGQEYS TLRTKHTESV ECDAPENSVV WQSSADDDKV  480
DVVSCSRRYG SENWMPSARH EPTYTDLLSG FGANIEPSHG QRIPFYDHSS SPSMPAKNIL  540
SDPEGKFDFL ANQWQMMQSG LSLKLHESPK VPAATDASFQ GRGNVKYSEY PVLNGLSTEN  600
AGGNWPIRPR ALNYYEEVVH AQAQAQAQAQ AREQATKQPV TIQEETAKSR EGNCRLFGIP  660
LSNNMNGTDS AMSQRSNLND AAGLTQLASP KVQDLPDQSK GSKSTNDHRE QGRPFQTNNP  720
HPKDAHTKSN SSRSCTKVHK QGIALGRSVD LSKFQNYEEL IAELDRLFEF NGELMAPKKD  780
WLIVYTDDEN DMMLVGDDPW QEFCCMVRKI FIYTKEEVRK MNPGTLSCRS EEGVVGEGSD  840
AKDAKSASNP SLSSAGNS*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A0.05339018354Auxin response factor 1
4ldw_A0.05339018354Auxin response factor 1
4ldw_B0.05339018354Auxin response factor 1
4ldx_A0.05339018354Auxin response factor 1
4ldx_B0.05339018354Auxin response factor 1
Search in ModeBase
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. 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}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00574DAPTransfer from AT5G62000Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMap919450
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK2212520.0AK221252.1 Arabidopsis thaliana mRNA for ARF1-binding protein, complete cds, clone: RAFL24-07-O11.
GenBankAK2212540.0AK221254.1 Arabidopsis thaliana mRNA for ARF1-binding protein, complete cds, clone: RAFL24-09-L23.
GenBankAK2212740.0AK221274.1 Arabidopsis thaliana mRNA for ARF1-binding protein, complete cds, clone: RAFL24-16-M02.
GenBankAK2213050.0AK221305.1 Arabidopsis thaliana mRNA for ARF1-binding protein, complete cds, clone: RAFL24-31-F22.
GenBankBT0007840.0BT000784.1 Arabidopsis thaliana clone RAFL07-10-G12 (R10939) auxin response factor (At5g62000) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_002864764.20.0LOW QUALITY PROTEIN: auxin response factor 2
SwissprotQ94JM30.0ARFB_ARATH; Auxin response factor 2
TrEMBLD7MKQ00.0D7MKQ0_ARALL; Auxin response factor
STRINGscaffold_802850.10.0(Arabidopsis lyrata)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM53482647
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G62000.30.0auxin response factor 2
Publications ? help Back to Top
  1. Chao WS,Doğramaci M,Foley ME,Horvath DP,Anderson JV
    Selection and validation of endogenous reference genes for qRT-PCR analysis in leafy spurge (Euphorbia esula).
    PLoS ONE, 2012. 7(8): p. e42839
    [PMID:22916167]
  2. Ozerova LV,Krasnikova MS,Troitsky AV,Solovyev AG,Morozov SY
    TAS3 Genes for small ta-siARF RNAs in plants belonging to subtribe Senecioninae: occurrence of prematurely terminated RNA precursors.
    Mol. Gen. Mikrobiol. Virusol., 2013.
    [PMID:24003511]
  3. Li C, et al.
    Ectopic expression of a maize hybrid down-regulated gene ZmARF25 decreases organ size by affecting cellular proliferation in Arabidopsis.
    PLoS ONE, 2014. 9(4): p. e94830
    [PMID:24756087]
  4. Lyons R, et al.
    Fusarium oxysporum triggers tissue-specific transcriptional reprogramming in Arabidopsis thaliana.
    PLoS ONE, 2015. 10(4): p. e0121902
    [PMID:25849296]
  5. Roodbarkelari F,Du F,Truernit E,Laux T
    ZLL/AGO10 maintains shoot meristem stem cells during Arabidopsis embryogenesis by down-regulating ARF2-mediated auxin response.
    BMC Biol., 2015. 13: p. 74
    [PMID:26358077]
  6. Meng LS,Wang ZB,Yao SQ,Liu A
    The ARF2-ANT-COR15A gene cascade regulates ABA-signaling-mediated resistance of large seeds to drought in Arabidopsis.
    J. Cell. Sci., 2015. 128(21): p. 3922-32
    [PMID:26395398]
  7. Zhao S,Zhang ML,Ma TL,Wang Y
    Phosphorylation of ARF2 Relieves Its Repression of Transcription of the K+ Transporter Gene HAK5 in Response to Low Potassium Stress.
    Plant Cell, 2016. 28(12): p. 3005-3019
    [PMID:27895227]
  8. Promchuea S,Zhu Y,Chen Z,Zhang J,Gong Z
    ARF2 coordinates with PLETHORAs and PINs to orchestrate ABA-mediated root meristem activity in Arabidopsis .
    J Integr Plant Biol, 2017. 59(1): p. 30-43
    [PMID:28074634]
  9. 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]
  10. Sanz-Fernández M, et al.
    Screening Arabidopsis mutants in genes useful for phytoremediation.
    J. Hazard. Mater., 2017. 335: p. 143-151
    [PMID:28441590]
  11. Zhang M,Hu X,Zhu M,Xu M,Wang L
    Transcription factors NF-YA2 and NF-YA10 regulate leaf growth via auxin signaling in Arabidopsis.
    Sci Rep, 2017. 7(1): p. 1395
    [PMID:28469131]
  12. Guan C, et al.
    Spatial Auxin Signaling Controls Leaf Flattening in Arabidopsis.
    Curr. Biol., 2017. 27(19): p. 2940-2950.e4
    [PMID:28943086]
  13. Liu Z, et al.
    ARF2-ARF4 and ARF5 are Essential for Female and Male Gametophyte Development in Arabidopsis.
    Plant Cell Physiol., 2018. 59(1): p. 179-189
    [PMID:29145642]
  14. Sarkar Das S, et al.
    Expression dynamics of miRNAs and their targets in seed germination conditions reveals miRNA-ta-siRNA crosstalk as regulator of seed germination.
    Sci Rep, 2018. 8(1): p. 1233
    [PMID:29352229]