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 Pp3c1_40270V3.11.p
Common NamePHYPADRAFT_168019
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: 888aa    MW: 98726.5 Da    PI: 6.8153
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pp3c1_40270V3.11.pgenomeCOSMOSSView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B377.61.4e-24137238199
                         EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE CS
                  B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkl 84 
                         f+k+lt sd++++g +++p++ ae+        + +++  ++l+ +d++ ++W +++iyr++++r++lt+GW+ Fv+a++L++gD v+F  
  Pp3c1_40270V3.11.p 137 FCKTLTASDTSTHGGFSIPRRAAEKVfppldysQTPPA--QELKARDLHDQEWHFRHIYRGQPRRHLLTTGWSVFVSAKRLQAGDAVLFI- 224
                         99****************************97544444..48************************************************. PP

                         -SSSEE..EEEEE-S CS
                  B3  85 dgrsefelvvkvfrk 99 
                          ++++++l ++++r+
  Pp3c1_40270V3.11.p 225 -RDDKGQLQLGIRRQ 238
                         .5578989****997 PP
2Auxin_resp117.79.5e-39263346183
          Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalk.vkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                         a haa+t+s F+++YnPr+s+seFv++v+k++ka+   +vsvGmRf+m fete+ss rr++Gt++g+ dldp+rWpnS+WrsLk
  Pp3c1_40270V3.11.p 263 ANHAAATSSRFTIFYNPRQSPSEFVIPVAKYQKAICnLQVSVGMRFRMVFETEESSVRRYMGTITGMGDLDPIRWPNSHWRSLK 346
                         679*******************************9658********************************************96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019362.09E-48126266IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.107.8E-43130252IPR015300DNA-binding pseudobarrel domain
CDDcd100174.85E-23136237No hitNo description
SMARTSM010191.7E-23137239IPR003340B3 DNA binding domain
PfamPF023621.6E-22137238IPR003340B3 DNA binding domain
PROSITE profilePS5086312.999137239IPR003340B3 DNA binding domain
PfamPF065072.0E-34263346IPR010525Auxin response factor
PROSITE profilePS5174524.674752836IPR000270PB1 domain
SuperFamilySSF542772.88E-8765831No hitNo description
PfamPF023092.2E-6797837IPR033389AUX/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:0009908Biological Processflower development
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0005515Molecular Functionprotein binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000006anatomyplant protoplast
PO:0025017anatomyplant spore
PO:0030003anatomyprotonema
PO:0030018anatomygametophore
Sequence ? help Back to Top
Protein Sequence    Length: 888 aa     Download sequence    Send to blast
MYQCSERPPN LVSGSGSKAQ LMEHMERRSP TSELWHACAG PLVSLPPIGS RVVYFPQGHT  60
EQVAASTQRE AETHIPNYPS LPSRLVCLLD NVTLHADLET DEVYAQMTLI PVPPANEKEA  120
LMSPDIGIRS RQPTDYFCKT LTASDTSTHG GFSIPRRAAE KVFPPLDYSQ TPPAQELKAR  180
DLHDQEWHFR HIYRGQPRRH LLTTGWSVFV SAKRLQAGDA VLFIRDDKGQ LQLGIRRQNR  240
QQTVMPSSVL SSDSMHIGVL AAANHAAATS SRFTIFYNPR QSPSEFVIPV AKYQKAICNL  300
QVSVGMRFRM VFETEESSVR RYMGTITGMG DLDPIRWPNS HWRSLKVGWD ESTAGERQRR  360
VSLWEIEPLT TPFLLCPPPL TFRAKRPWGG RVDEEMDSML KKASFWSGDS GSHMDALGAL  420
NLRNFGMSSW MRTPQQRVEP GLPAQQNEYY RAFAAAALQE IRCSDASKHA MSHAQPSLST  480
SQIEFRSQSP QSNQHTAQHI PNTAGPVLQL SSSRPESPLD VGMNMAQCSG YSESDTHMTS  540
SAYTPGSYPL HSMLGRTHLG CENGQMTYMM RPTQSAQQSQ PESIIHGGSV REPQFSSSWY  600
PSNRDTSEHD VSARMNQLDT SPTSRVSSCF PFPQESQVNG QSGLTGLPVP TSSFVYRENG  660
QEQDSVQSDR HLLFGVSIEQ PLVGSNSVTS LQPHAFAKSK DPQSRFSGNT VLQGSYYPSG  720
NADIPTMNGV GLDENGIFMR NASWSAMAPT SRTFTKVHKL GSVGRSIDVQ KFQNYSELRV  780
ELARLFNLEG LLDDPQRSGW QLVFVDNEND TLLVGDDPWE EFVNCVRSIK ILSPNEILQM  840
SQEQLEILNS VPMQQRPTCS NSEDARTQTS PVNTSNLSME HGHSGGR*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldu_A1e-1621736729388Auxin response factor 5
Search in ModeBase
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_024385779.10.0auxin response factor 6-like isoform X1
RefseqXP_024385788.10.0auxin response factor 6-like isoform X1
RefseqXP_024385797.10.0auxin response factor 6-like isoform X1
SwissprotQ9ZTX80.0ARFF_ARATH; Auxin response factor 6
TrEMBLA0A2K1LBN00.0A0A2K1LBN0_PHYPA; Auxin response factor
STRINGPP1S163_119V6.10.0(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. Rensing SA, et al.
    The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants.
    Science, 2008. 319(5859): p. 64-9
    [PMID:18079367]
  2. 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]
  3. Oh E, et al.
    Cell elongation is regulated through a central circuit of interacting transcription factors in the Arabidopsis hypocotyl.
    Elife, 2015.
    [PMID:24867218]
  4. 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]
  5. 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]
  6. 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]
  7. 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]
  8. 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]
  9. 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]
  10. 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]
  11. 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]
  12. 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]
  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]