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_40270V3.1.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: 886aa    MW: 98498.2 Da    PI: 6.6638
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pp3c1_40270V3.1.pgenomeCOSMOSSView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B377.61.4e-24135236199
                        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+ Fv+a++L++gD v+F   
  Pp3c1_40270V3.1.p 135 FCKTLTASDTSTHGGFSIPRRAAEKVfppldysQTPPA--QELKARDLHDQEWHFRHIYRGQPRRHLLTTGWSVFVSAKRLQAGDAVLFI-- 222
                        99****************************97544444..48************************************************.. PP

                        SSSEE..EEEEE-S CS
                 B3  86 grsefelvvkvfrk 99 
                        ++++++l ++++r+
  Pp3c1_40270V3.1.p 223 RDDKGQLQLGIRRQ 236
                        5578989****997 PP
2Auxin_resp117.79.5e-39261344183
         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_40270V3.1.p 261 ANHAAATSSRFTIFYNPRQSPSEFVIPVAKYQKAICnLQVSVGMRFRMVFETEESSVRRYMGTITGMGDLDPIRWPNSHWRSLK 344
                        679*******************************9658********************************************96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019362.09E-48124264IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.107.7E-43128250IPR015300DNA-binding pseudobarrel domain
CDDcd100174.83E-23134235No hitNo description
SMARTSM010191.7E-23135237IPR003340B3 DNA binding domain
PfamPF023621.6E-22135236IPR003340B3 DNA binding domain
PROSITE profilePS5086312.999135237IPR003340B3 DNA binding domain
PfamPF065072.0E-34261344IPR010525Auxin response factor
PROSITE profilePS5174524.674750834IPR000270PB1 domain
SuperFamilySSF542772.81E-8763829No hitNo description
PfamPF023092.2E-6795835IPR033389AUX/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: 886 aa     Download sequence    Send to blast
MEVVAEEESR PCGATVWSGF LRVERRSPTS ELWHACAGPL VSLPPIGSRV VYFPQGHTEQ  60
VAASTQREAE THIPNYPSLP SRLVCLLDNV TLHADLETDE VYAQMTLIPV PPANEKEALM  120
SPDIGIRSRQ PTDYFCKTLT ASDTSTHGGF SIPRRAAEKV FPPLDYSQTP PAQELKARDL  180
HDQEWHFRHI YRGQPRRHLL TTGWSVFVSA KRLQAGDAVL FIRDDKGQLQ LGIRRQNRQQ  240
TVMPSSVLSS DSMHIGVLAA ANHAAATSSR FTIFYNPRQS PSEFVIPVAK YQKAICNLQV  300
SVGMRFRMVF ETEESSVRRY MGTITGMGDL DPIRWPNSHW RSLKVGWDES TAGERQRRVS  360
LWEIEPLTTP FLLCPPPLTF RAKRPWGGRV DEEMDSMLKK ASFWSGDSGS HMDALGALNL  420
RNFGMSSWMR TPQQRVEPGL PAQQNEYYRA FAAAALQEIR CSDASKHAMS HAQPSLSTSQ  480
IEFRSQSPQS NQHTAQHIPN TAGPVLQLSS SRPESPLDVG MNMAQCSGYS ESDTHMTSSA  540
YTPGSYPLHS MLGRTHLGCE NGQMTYMMRP TQSAQQSQPE SIIHGGSVRE PQFSSSWYPS  600
NRDTSEHDVS ARMNQLDTSP TSRVSSCFPF PQESQVNGQS GLTGLPVPTS SFVYRENGQE  660
QDSVQSDRHL LFGVSIEQPL VGSNSVTSLQ PHAFAKSKDP QSRFSGNTVL QGSYYPSGNA  720
DIPTMNGVGL DENGIFMRNA SWSAMAPTSR TFTKVHKLGS VGRSIDVQKF QNYSELRVEL  780
ARLFNLEGLL DDPQRSGWQL VFVDNENDTL LVGDDPWEEF VNCVRSIKIL SPNEILQMSQ  840
EQLEILNSVP MQQRPTCSNS EDARTQTSPV NTSNLSMEHG HSGGR*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldu_A1e-1623036553388Auxin 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_024385815.10.0auxin response factor 6-like isoform X3
SwissprotQ9ZTX80.0ARFF_ARATH; Auxin response factor 6
TrEMBLA0A2K1LBN00.0A0A2K1LBN0_PHYPA; Auxin response factor
STRINGPP1S163_119V6.10.0(Physcomitrella patens)
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]