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 Pavir.5KG746900.3.p
Organism
Panicum virgatum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Panicodae; Paniceae; Panicinae; Panicum
Family ARF
Protein Properties Length: 753aa    MW: 84659.8 Da    PI: 6.6828
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.5KG746900.3.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B373.42.7e-2371172199
                          EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEE CS
                   B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFk 83 
                          f+k+lt sd++++g +++ +++a+e+       +++++  ++l+ +d++g +W++++i+r++++r++l++GW+ Fv++++L +gD ++F 
  Pavir.5KG746900.3.p  71 FCKTLTASDTSTHGGFSVLRRHADEClppldmtQSPPT--QELVAKDLHGMEWRFRHIFRGQPRRHLLQSGWSVFVSSKRLVAGDAFIFL 158
                          99*****************************7555544..58************************************************ PP

                          E-SSSEE..EEEEE-S CS
                   B3  84 ldgrsefelvvkvfrk 99 
                            + +++el+v+v+r+
  Pavir.5KG746900.3.p 159 --RGENGELRVGVRRA 172
                          ..449999*****996 PP
2Auxin_resp108.19.7e-36197278183
           Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                          a+ha++tks+F+v+Y+Pr+s+seF++++++++++lk+++s+G Rf+m+fe+e+++e+r++Gt+vg  +ldp  Wp+S Wr Lk
  Pavir.5KG746900.3.p 197 AWHAINTKSMFTVYYKPRTSPSEFIIPYDQYMESLKNNYSIGLRFRMRFEGEEAPEQRFTGTIVGCDNLDP-LWPDSSWRYLK 278
                          89*********************************************************************.9*******996 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.101.1E-4062186IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019367.32E-4064200IPR015300DNA-binding pseudobarrel domain
CDDcd100173.35E-2169171No hitNo description
PfamPF023623.6E-2171172IPR003340B3 DNA binding domain
SMARTSM010191.8E-2371173IPR003340B3 DNA binding domain
PROSITE profilePS5086311.92871173IPR003340B3 DNA binding domain
PfamPF065073.0E-32197278IPR010525Auxin response factor
PfamPF023091.2E-5623676IPR033389AUX/IAA domain
SuperFamilySSF542774.41E-13634717No hitNo description
PROSITE profilePS5174524.965640733IPR000270PB1 domain
PfamPF023093.8E-8685725IPR033389AUX/IAA domain
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: 753 aa     Download sequence    Send to blast
MNQVAGNQMR IYDLPSKLLC RVLNVELKAE TETDEVYAQI MLMPEPEQNE VAAEKSSSGA  60
AATPRPAVRS FCKTLTASDT STHGGFSVLR RHADECLPPL DMTQSPPTQE LVAKDLHGME  120
WRFRHIFRGQ PRRHLLQSGW SVFVSSKRLV AGDAFIFLRG ENGELRVGVR RAMRQLSNVP  180
SSVISSQSMH LGVLATAWHA INTKSMFTVY YKPRTSPSEF IIPYDQYMES LKNNYSIGLR  240
FRMRFEGEEA PEQRFTGTIV GCDNLDPLWP DSSWRYLKVR WDEPSTIPRP DRVSPWKIEP  300
ASSPPVNPLP LSSRVKRPRQ APPPSPESSV LTKEGASKID ISSAQTQQHQ NSVLQGQEQM  360
TLRNNMTEST DSDATVQKPM MWSPSPNGKT HTSFQQRPSM DNWMPMGRRE TDFKDTRSAF  420
KDARTSSQSF GDTQGFFMPT FDENHHRLSF NNQFQDQGSA HRFSDPYFYM PQQPSLTVDS  480
STRMQSASNE LRFWSEQNTV YGNSNDQQKG FTFAQNPSSW LNQPFPQVEQ PRVVRPHATV  540
APFDLEKTRE GSGFKIFGFK VDAASASPIQ LTSPMSTMRE HVVQTQPPAS VNELQPVQTE  600
CLPEGSVSTA GTATENEKSI QQAPQSSKDI QSKSQGASTR SCTKVHKQGV ALGRSVDLSK  660
FGDYDELKAE LDKMFEFEGE LVSANKNWQI VYTDNEGDMM LVGDDPWEEF CSIVRKIYIY  720
TKEEVQKMNS KSSAPRKEEP LASGEVCAAT NE*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-142130356357Auxin response factor 1
4ldw_A1e-142130356357Auxin response factor 1
4ldw_B1e-142130356357Auxin response factor 1
4ldx_A1e-142130356357Auxin response factor 1
4ldx_B1e-142130356357Auxin response factor 1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.3460.0callus| leaf| root| stem
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in roots, culms, leaves and young panicles. {ECO:0000269|PubMed:17408882}.
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).
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.5KG746900.3.p
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_025815802.10.0auxin response factor 4-like
SwissprotQ5JK200.0ARFD_ORYSJ; Auxin response factor 4
TrEMBLA0A2T7DC640.0A0A2T7DC64_9POAL; Auxin response factor
STRINGPavir.Ea03860.1.p0.0(Panicum virgatum)
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. Kikuchi S, et al.
    Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice.
    Science, 2003. 301(5631): p. 376-9
    [PMID:12869764]
  2. Song X, et al.
    Rice RNA-dependent RNA polymerase 6 acts in small RNA biogenesis and spikelet development.
    Plant J., 2012. 71(3): p. 378-89
    [PMID:22443269]
  3. Kishimoto N, et al.
    Identification of the duplicated segments in rice chromosomes 1 and 5 by linkage analysis of cDNA markers of known functions.
    Theor. Appl. Genet., 1994. 88(6-7): p. 722-6
    [PMID:24186168]