PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Pp3c1_14440V3.1.p
Common NamePHYPADRAFT_131154
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Bryophyta; Bryophytina; Bryopsida; Funariidae; Funariales; Funariaceae; Physcomitrella
Family ARF
Protein Properties Length: 284aa    MW: 32090.6 Da    PI: 9.3108
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pp3c1_14440V3.1.pgenomeCOSMOSSView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B357.91.9e-1875157199
                        EEEE-..-HHHHTT-EE--HHH.HTT---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE.. CS
                 B3   1 ffkvltpsdvlksgrlvlpkkfaeehggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefel 92 
                        f+k+lt sd++++g +++p++ ae+   +     t          W +++iyr++++r++lt+GW+ Fv+a++L++gD v+F   ++++++l
  Pp3c1_14440V3.1.p  75 FCKTLTASDTSTHGGFSIPRRAAEKVF-P-----T--------LDWHFRHIYRGQPRRHLLTTGWSVFVSAKRLQAGDAVLFI--RDDKGQL 150
                        99*********************8885.2.....2........34**************************************..5688999 PP

                        EEEEE-S CS
                 B3  93 vvkvfrk 99 
                        +++++r+
  Pp3c1_14440V3.1.p 151 LLGIRRA 157
                        ****997 PP

2Auxin_resp120.71.1e-39182265183
         Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalk.vkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                        a+haa+t+s F+++YnPr+s+seFv++++k++ka++ ++v+vGmRf+m fete+s  rr++Gtv+g+ dldpvrWpnS+WrsLk
  Pp3c1_14440V3.1.p 182 ASHAAQTSSRFTIFYNPRQSPSEFVIPLAKYQKAVYsTQVTVGMRFRMVFETEESTVRRYMGTVTGIGDLDPVRWPNSHWRSLK 265
                        789********************************989********************************************96 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019365.36E-4059185IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.107.1E-3067171IPR015300DNA-binding pseudobarrel domain
CDDcd100171.69E-1974156No hitNo description
SMARTSM010191.0E-1475158IPR003340B3 DNA binding domain
PfamPF023621.7E-1675157IPR003340B3 DNA binding domain
PROSITE profilePS5086310.546106158IPR003340B3 DNA binding domain
PfamPF065077.4E-35182265IPR010525Auxin response factor
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
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0030018anatomygametophore
Sequence ? help Back to Top
Protein Sequence    Length: 284 aa     Download sequence    Send to blast
MVAVSTQKEA DTHIPNYPNL RPHLVCTLDN ITLHADLETD EVYAQMVLIP SQDPDKETML  60
LPDAVVQNKQ PTEYFCKTLT ASDTSTHGGF SIPRRAAEKV FPTLDWHFRH IYRGQPRRHL  120
LTTGWSVFVS AKRLQAGDAV LFIRDDKGQL LLGIRRANRL QTMMPSSVLS SDSMHIGILA  180
AASHAAQTSS RFTIFYNPRQ SPSEFVIPLA KYQKAVYSTQ VTVGMRFRMV FETEESTVRR  240
YMGTVTGIGD LDPVRWPNSH WRSLKVGWDE STAGERQLRV SLW*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldu_A1e-129228384385Auxin 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_024373311.10.0auxin response factor 5-like
RefseqXP_024373320.10.0auxin response factor 5-like
SwissprotQ9ZTX81e-147ARFF_ARATH; Auxin response factor 6
TrEMBLA0A2K1L8560.0A0A2K1L856_PHYPA; Auxin response factor
STRINGPP1S86_4V6.10.0(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
AT1G30330.21e-150auxin 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]