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 Potri.003G163600.1
Common NamePOPTR_0003s16210g
Organism
Populus trichocarpa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus
Family ARF
Protein Properties Length: 805aa    MW: 91411.6 Da    PI: 7.1637
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Potri.003G163600.1genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B371.88.7e-23159260199
                         EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE- CS
                  B3   1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkld 85 
                         f+k lt sd++++g +++ k++a+e+      +++++  ++l+ +d++g++W++++i+r++++r++l++GW+ Fv+a++L +gD ++F   
  Potri.003G163600.1 159 FCKMLTASDTSTHGGFSVLKRHADEClppldmSLQPPV-QELVAKDLHGNEWRFRHIFRGQPRRHLLQSGWSLFVSAKKLVAGDAFIFL-- 246
                         89*****************************9666655.49************************************************.. PP

                         SSSEE..EEEEE-S CS
                  B3  86 grsefelvvkvfrk 99 
                         + +++el+v+v+r+
  Potri.003G163600.1 247 RGETEELRVGVRRA 260
                         3489999****985 PP
2Auxin_resp119.13.6e-39285367183
          Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                         a+ha+st+s+F+v+Y+Pr+s++eF+++v+k+++++k+++++GmRfkm+fe +d++e+r+sGtv+gv+++dp +Wp+S+Wr+Lk
  Potri.003G163600.1 285 AWHAVSTGSMFTVYYKPRTSPAEFIIPVDKYMESVKINYAIGMRFKMRFEADDAPEQRFSGTVIGVEEADPKKWPRSNWRCLK 367
                         89*******************************************************************************96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019365.89E-39152288IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.108.6E-39153274IPR015300DNA-binding pseudobarrel domain
CDDcd100171.13E-19157259No hitNo description
PROSITE profilePS5086311.42159261IPR003340B3 DNA binding domain
SMARTSM010191.4E-21159261IPR003340B3 DNA binding domain
PfamPF023629.9E-21159260IPR003340B3 DNA binding domain
PfamPF065079.9E-36285367IPR010525Auxin response factor
PROSITE profilePS5174524.355657750IPR000270PB1 domain
SuperFamilySSF542775.4E-11657734No hitNo description
PfamPF023095.1E-6703748IPR033389AUX/IAA 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:0005515Molecular Functionprotein binding
Sequence ? help Back to Top
Protein Sequence    Length: 805 aa     Download sequence    Send to blast
MELRAGAGVF RWLVKVPMII HNDFLSFSFD FFRFYWIIAV VVLARVGSED ALYKELWHAC  60
AGPLVTVPRQ GELVYYFPQG HIEQVEASTN QVADDQQMPA YNLSPKILCR VVNVQLKAEL  120
DTDEVFAQVI LLPETQQDVE LVEEEDLPPL PARPRVHSFC KMLTASDTST HGGFSVLKRH  180
ADECLPPLDM SLQPPVQELV AKDLHGNEWR FRHIFRGQPR RHLLQSGWSL FVSAKKLVAG  240
DAFIFLRGET EELRVGVRRA LRQPSKIPSS LISSHSMHIG ILATAWHAVS TGSMFTVYYK  300
PRTSPAEFII PVDKYMESVK INYAIGMRFK MRFEADDAPE QRFSGTVIGV EEADPKKWPR  360
SNWRCLKVHW DETSPVHRPD RVSPWKVEPA LAPSMDPVSG CRLKRHRPNT VTSSADSSAL  420
TKKDNGPSRH MQHQEILTLR NTPTGKNYSD NNHNPPWVLS QGTGTLLKSY ESSRPFFGLF  480
SDDVDQPSKL TSDEKSMFNW HSAPMMYTGH PFNMLASSME VQVAKDKDTQ QQHGSRFLPF  540
PYADSSPHPS RSKPQHLPFQ QCNERTAKDD NYKLFGVSLF RNSKALEPAT IHRHSADKPQ  600
HQINVASDHL QLLGSDRYLE QLKHPKHARC EEQENIFQAS SLYSKDVQGK PEGGSARRCV  660
KVHKQGTAVG RSLDLAKFNG YNELTAELDQ IFEFNGELVA PNKDWLIVFT DDEDDMMLVG  720
DDPWQEFCSM ARRIFIYTKE EINRMEPRSL NREAEGNSRS TDQMVDLENR ISKHLPAVSP  780
SECQGLCYMT GSKVRDASTW IPKP*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-1655038917354Auxin response factor 1
4ldw_A1e-1655038917354Auxin response factor 1
4ldw_B1e-1655038917354Auxin response factor 1
4ldx_A1e-1655038917354Auxin response factor 1
4ldx_B1e-1655038917354Auxin response factor 1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pth.117330.0bud
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
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPotri.003G163600.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC2084820.0AC208482.1 Populus trichocarpa clone JGIACSB13-H05, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_002303753.30.0auxin response factor 2 isoform X2
SwissprotQ94JM30.0ARFB_ARATH; Auxin response factor 2
TrEMBLA0A385JHW80.0A0A385JHW8_POPTO; Auxin response factor
STRINGPOPTR_0003s16210.10.0(Populus trichocarpa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF32813366
Representative plantOGRP5501582
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G62000.40.0auxin 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]