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 Pp3c2_25890V3.1.p
Organism
Physcomitrella patens
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Bryophyta; Bryophytina; Bryopsida; Funariidae; Funariales; Funariaceae; Physcomitrella
Family ARF
Protein Properties Length: 775aa    MW: 85876.8 Da    PI: 6.7998
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pp3c2_25890V3.1.pgenomeCOSMOSSView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B373.72.2e-23130231199
                        EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE- CS
                 B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkld 85 
                        f+k+lt sd++++g +++p++ ae+        ++++++  +l+ +d++ + W +++iyr++++r++lt+GW+ F +a++L++gD v+F   
  Pp3c2_25890V3.1.p 130 FCKTLTASDTSTHGGFSIPRRAAEKVfptldytQQPPAQ--ELVARDLHDQDWHFRHIYRGQPRRHLLTTGWSIFISAKRLQAGDAVLFI-- 217
                        99*****************************96555555..8************************************************.. PP

                        SSSEE..EEEEE-S CS
                 B3  86 grsefelvvkvfrk 99 
                        ++++++l+++++r+
  Pp3c2_25890V3.1.p 218 RDDKGQLLLGIRRA 231
                        5588999****997 PP
2Auxin_resp118.26.8e-39256339183
         Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalk.vkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                        a+haa+t+s F+++YnPr+s+seFv++ +k++ka++ ++++vGmRf+m+fete+s  rr++Gtv+g+ dldpvrWpnS+WrsLk
  Pp3c2_25890V3.1.p 256 ASHAAQTSSRFTIFYNPRQSPSEFVIPSAKYQKAVYsTQITVGMRFRMMFETEESTVRRYMGTVTGIGDLDPVRWPNSHWRSLK 339
                        789********************************989********************************************96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019367.32E-50114259IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.106.7E-40122245IPR015300DNA-binding pseudobarrel domain
CDDcd100171.02E-20129230No hitNo description
SMARTSM010196.4E-21130232IPR003340B3 DNA binding domain
PROSITE profilePS5086312.83130232IPR003340B3 DNA binding domain
PfamPF023623.5E-21130231IPR003340B3 DNA binding domain
PfamPF065074.0E-34256339IPR010525Auxin response factor
PROSITE profilePS5174525.565651735IPR000270PB1 domain
PfamPF023092.3E-6654737IPR033389AUX/IAA domain
SuperFamilySSF542778.53E-7665730No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009725Biological Processresponse to hormone
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0005515Molecular Functionprotein binding
Sequence ? help Back to Top
Protein Sequence    Length: 775 aa     Download sequence    Send to blast
MYSHVPMRGS GFASSTIVQG EKRINSELWH ACAGPLVSLP PVGSQVVYFP QGHSEQVAVS  60
TQKEADIHIP NYPNLRPHLI CTLENVTLHA DLETDDVYAQ MVLIPTQDPE KETMLLPDVV  120
VQNKQPTEYF CKTLTASDTS THGGFSIPRR AAEKVFPTLD YTQQPPAQEL VARDLHDQDW  180
HFRHIYRGQP RRHLLTTGWS IFISAKRLQA GDAVLFIRDD KGQLLLGIRR ANRLQTIMPS  240
SVLSSDSMHI GILAAASHAA QTSSRFTIFY NPRQSPSEFV IPSAKYQKAV YSTQITVGMR  300
FRMMFETEES TVRRYMGTVT GIGDLDPVRW PNSHWRSLKV GWDESTAGER QRRVSLWEIE  360
PLTTPFLICP PPIVLRSKRA RGIHGEDEDL ETLMKKSPMW PSLGFGTDSP WMGILPQRPG  420
HGVTSSLNEY NRTLAVAASQ EFREPSKQVV TESMSNPQNL YRQQQLQTQQ HSHRNPQSIA  480
QINDVPGPLL QLSTSQASID LGSSVRPISS YSDSEIYVSS PSPRPFSTQA MMSRIPGNVP  540
VSSADGNQFP SLMRTNQNGL PLYGSVTGNH QVSSSWLPTL QNQSQAEPQS ASPRFHRAEA  600
SIGGGVPGLY GPIQHGEAGD AGILPNEALD ENIMLQRNVG WPAVATAPPV RSFTKVHKLG  660
SVGRSLDINK FSNYVELRKE LAHMFHLECL MEDSQQSSWK IVFVDNENDT LLLGDEPWEE  720
FVSCVRSIKI LSPAEVAQMN QHVLAAVSGQ HLRPSNSNSE DTPSSQAGVG VVDH*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldu_A1e-1612436051388Auxin response factor 5
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Ppa.168710.0protonema
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed in sepals at stages 11, 12 and 13 of flower development. Highly expressed in petals at stages 9-10, decreases at stage 11 and disappears after flower stage 12. In anthers, expressed at stage 11 in the tapetum, disappears early in stage 12 when the tapetum degrades and reappears throughout the anther late in stage 12 to persist at least until stage 13. In stamen filaments, expressed at stages 12 to 13, especially near the apical end of the filament. Expressed throughout the gynoecium at early stages up to stage 12, especially strongly in ovules. Expression in gynoecium decreases late in stage 12, but persists through stage 13, especially near the apical end including the style. {ECO:0000269|PubMed:16107481}.
UniprotTISSUE SPECIFICITY: Expressed in the whole plant. {ECO:0000269|PubMed:10476078}.
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). Seems to act as transcriptional activator. Formation of heterodimers with Aux/IAA proteins may alter their ability to modulate early auxin response genes expression. Regulates both stamen and gynoecium maturation. Promotes jasmonic acid production. Partially redundant with ARF8. {ECO:0000269|PubMed:12036261, ECO:0000269|PubMed:16107481}.
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Repressed by miR167. {ECO:0000269|PubMed:17021043}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_024359915.10.0auxin response factor 6-like isoform X3
SwissprotQ9ZTX80.0ARFF_ARATH; Auxin response factor 6
TrEMBLA0A2K1L3020.0A0A2K1L302_PHYPA; Auxin response factor
STRINGPP1S119_32V6.20.0(Physcomitrella patens)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP8561456
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G30330.20.0auxin response factor 6
Publications ? help Back to Top
  1. Liu N, et al.
    Down-regulation of AUXIN RESPONSE FACTORS 6 and 8 by microRNA 167 leads to floral development defects and female sterility in tomato.
    J. Exp. Bot., 2014. 65(9): p. 2507-20
    [PMID:24723401]
  2. Oh E, et al.
    Cell elongation is regulated through a central circuit of interacting transcription factors in the Arabidopsis hypocotyl.
    Elife, 2015.
    [PMID:24867218]
  3. Minato N, et al.
    The phytoplasmal virulence factor TENGU causes plant sterility by downregulating of the jasmonic acid and auxin pathways.
    Sci Rep, 2014. 4: p. 7399
    [PMID:25492247]
  4. Ortega-Amaro MA, et al.
    Overexpression of AtGRDP2, a novel glycine-rich domain protein, accelerates plant growth and improves stress tolerance.
    Front Plant Sci, 2014. 5: p. 782
    [PMID:25653657]
  5. Asahina M,Satoh S
    Molecular and physiological mechanisms regulating tissue reunion in incised plant tissues.
    J. Plant Res., 2015. 128(3): p. 381-8
    [PMID:25736731]
  6. Batista VG,Pinheiro MP,Melo Filho PA,Santos RC,Lima LM
    Temporal and tissue expression of genes involved in buds of earliness cotton cultivar.
    Genet. Mol. Res., 2015. 14(3): p. 7386-94
    [PMID:26214417]
  7. Li P, et al.
    Ca(2+) -regulated and diurnal rhythm-regulated Na(+) /Ca(2+) exchanger AtNCL affects flowering time and auxin signalling in Arabidopsis.
    Plant Cell Environ., 2016. 39(2): p. 377-92
    [PMID:26296956]
  8. Barik S, et al.
    Coevolution Pattern and Functional Conservation or Divergence of miR167s and their targets across Diverse Plant Species.
    Sci Rep, 2015. 5: p. 14611
    [PMID:26459056]
  9. Luo S, et al.
    Constitutive Expression of OsIAA9 Affects Starch Granules Accumulation and Root Gravitropic Response in Arabidopsis.
    Front Plant Sci, 2015. 6: p. 1156
    [PMID:26734051]
  10. 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]
  11. Zhang GZ, et al.
    Ectopic expression of UGT84A2 delayed flowering by indole-3-butyric acid-mediated transcriptional repression of ARF6 and ARF8 genes in Arabidopsis.
    Plant Cell Rep., 2017. 36(12): p. 1995-2006
    [PMID:29027578]
  12. 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]