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 PSME_00022730-RA
Organism
Pseudotsuga menziesii
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Acrogymnospermae; Pinidae; Pinales; Pinaceae; Pseudotsuga
Family ARF
Protein Properties Length: 872aa    MW: 96862.7 Da    PI: 5.8971
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
PSME_00022730-RAgenomePRSView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B3758.9e-24167268199
                       EEEE-..-HHHHTT-EE--HHH.HTT.....---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSS CS
                B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.....ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrs 88 
                       f+k+lt sd++++g +++ +++a+e+     +++++ s++l+ +d++g +W++++i+r++++r++lt+GW+ Fv++++L +gD ++F   + +
  PSME_00022730-RA 167 FCKTLTASDTSTHGGFSVLRRHADEClpsldMSQQPPSQELVAKDLHGVEWRFRHIFRGQPRRHLLTTGWSVFVSSKRLVAGDAFIFL--RGE 257
                       99*****************************55566678*************************************************..449 PP

                       EE..EEEEE-S CS
                B3  89 efelvvkvfrk 99 
                       ++el+v+v+r+
  PSME_00022730-RA 258 NGELRVGVRRA 268
                       999*****996 PP
2Auxin_resp123.61.4e-40293375183
        Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                       a+ha+st+++F+v+Y+Pr+s+seF+++++++++a+k+++svGmRfkm+fe+e+++e+r++Gt+vg+ d+dpv+Wp+SkWr+Lk
  PSME_00022730-RA 293 ASHAVSTRTMFSVYYKPRTSPSEFIIPYDQYMEAMKTNFSVGMRFKMKFEGEEVPEQRFTGTIVGICDVDPVSWPGSKWRCLK 375
                       789******************************************************************************96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.106.8E-42160282IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019362.09E-43161296IPR015300DNA-binding pseudobarrel domain
CDDcd100172.19E-21166267No hitNo description
PfamPF023621.2E-21167268IPR003340B3 DNA binding domain
SMARTSM010194.0E-23167269IPR003340B3 DNA binding domain
PROSITE profilePS5086312.012167269IPR003340B3 DNA binding domain
PfamPF065075.2E-38293375IPR010525Auxin response factor
PROSITE profilePS5174523.564757842IPR000270PB1 domain
SuperFamilySSF542775.89E-9759830No hitNo description
PfamPF023096.1E-5802846IPR033389AUX/IAA domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0008285Biological Processnegative regulation of cell proliferation
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: 872 aa     Download sequence    Send to blast
MAYAENFRNF TCRIPASNQS NSSNGGVDGY SSMPNEGGLV LGQIGGSHGY LNSSQSVNDA  60
LYEELWHACA GPLVTLPRIG ERVFYFPQGH MEQVEASTNQ GADQHMPLFN LPFKILCRVI  120
NVQLKAEADT DEVFSQITLV PEVEQDESSV DKEPLPPLAP KPLVYSFCKT LTASDTSTHG  180
GFSVLRRHAD ECLPSLDMSQ QPPSQELVAK DLHGVEWRFR HIFRGQPRRH LLTTGWSVFV  240
SSKRLVAGDA FIFLRGENGE LRVGVRRAMR QQNNVPSSVI SSHSMHLGVI ATASHAVSTR  300
TMFSVYYKPR TSPSEFIIPY DQYMEAMKTN FSVGMRFKMK FEGEEVPEQR FTGTIVGICD  360
VDPVSWPGSK WRCLKVQWDE ISAITRPERV SPWKLEPSLA PASVNSLPVA RGKRPRPNIL  420
PLSSDLSVLD KASVDSTQVH RFPRVLQGQE VMTLGGSLGD SDLESGQKTV VWGSKLDDVK  480
SEGMGCQRRL LSENWMPPLR HDSVYSDAFS SFQPMGEMQE FRGSLPNSIL EDAQQPKVSR  540
KQFQDQEGKI VDASGLWSTN FPNSLQEMSV TSAAQSHRQS GNARWPGLNG HPQFSNIGME  600
SLVGNWQMHM ISQCQSEASV AHGGADRNAA RTLQVNNMGG TEPQPSFDLW ETSKGAEVSR  660
PTDSNCKLFG FHLIDNSTGG ELNLSKIRGS VNEEDLQVAA HASTEIRSQS VEPEQQSEQT  720
KTTKSDVPAA SCEQEKTSPR SSNETQCRAS AQSNPMRSCT KVQKQGSALG RAVDLTKFEG  780
YTELIRELEL MFNFEGQLQD ASKGWQVVYT DDEGDMMLVG DDPWHREFCC MVRKIFIYTR  840
EEVEKMTPSA APNMKIPGHS EEEKVARETP TQ
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-1795739715354Auxin response factor 1
4ldw_A1e-1795739715354Auxin response factor 1
4ldw_B1e-1795739715354Auxin response factor 1
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1412416KRPRP
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
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankBT1165820.0BT116582.1 Picea glauca clone GQ03802_H23 mRNA sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_010942378.10.0auxin response factor 23
SwissprotQ94JM30.0ARFB_ARATH; Auxin response factor 2
TrEMBLA0A0C9RYI40.0A0A0C9RYI4_9SPER; Auxin response factor
STRINGXP_008776920.10.0(Phoenix dactylifera)
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]