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.5KG746900.1.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: 811aa    MW: 90807.8 Da    PI: 6.4229
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.5KG746900.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B373.33e-23129230199
                          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.5KG746900.1.p 129 FCKTLTASDTSTHGGFSVLRRHADEClppldmtQSPPT--QELVAKDLHGMEWRFRHIFRGQPRRHLLQSGWSVFVSSKRLVAGDAFIFL 216
                          99*****************************7555544..58************************************************ PP

                          E-SSSEE..EEEEE-S CS
                   B3  84 ldgrsefelvvkvfrk 99 
                            + +++el+v+v+r+
  Pavir.5KG746900.1.p 217 --RGENGELRVGVRRA 230
                          ..449999*****996 PP
2Auxin_resp107.91.1e-35255336183
           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.5KG746900.1.p 255 AWHAINTKSMFTVYYKPRTSPSEFIIPYDQYMESLKNNYSIGLRFRMRFEGEEAPEQRFTGTIVGCDNLDP-LWPDSSWRYLK 336
                          89*********************************************************************.9*******996 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.101.2E-40120244IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019368.24E-40122258IPR015300DNA-binding pseudobarrel domain
CDDcd100173.89E-21127229No hitNo description
SMARTSM010191.8E-23129231IPR003340B3 DNA binding domain
PfamPF023624.0E-21129230IPR003340B3 DNA binding domain
PROSITE profilePS5086311.928129231IPR003340B3 DNA binding domain
PfamPF065073.4E-32255336IPR010525Auxin response factor
PfamPF023091.3E-5681734IPR033389AUX/IAA domain
SuperFamilySSF542774.91E-13692775No hitNo description
PROSITE profilePS5174524.965698791IPR000270PB1 domain
PfamPF023094.2E-8743783IPR033389AUX/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: 811 aa     Download sequence    Send to blast
MPPAAMAPPP PPQAPSNSGD PLYPELWRAC AGPLVTVPRP GDLVFYFPQG HIEQVEASMN  60
QVAGNQMRIY DLPSKLLCRV LNVELKAETE TDEVYAQIML MPEPEQNEVA AEKSSSGAAA  120
TPRPAVRSFC KTLTASDTST HGGFSVLRRH ADECLPPLDM TQSPPTQELV AKDLHGMEWR  180
FRHIFRGQPR RHLLQSGWSV FVSSKRLVAG DAFIFLRGEN GELRVGVRRA MRQLSNVPSS  240
VISSQSMHLG VLATAWHAIN TKSMFTVYYK PRTSPSEFII PYDQYMESLK NNYSIGLRFR  300
MRFEGEEAPE QRFTGTIVGC DNLDPLWPDS SWRYLKVRWD EPSTIPRPDR VSPWKIEPAS  360
SPPVNPLPLS SRVKRPRQAP PPSPESSVLT KEGASKIDIS SAQTQQHQNS VLQGQEQMTL  420
RNNMTESTDS DATVQKPMMW SPSPNGKTHT SFQQRPSMDN WMPMGRRETD FKDTRSAFKD  480
ARTSSQSFGD TQGFFMPTFD ENHHRLSFNN QFQDQGSAHR FSDPYFYMPQ QPSLTVDSST  540
RMQSASNELR FWSEQNTVYG NSNDQQKGFT FAQNPSSWLN QPFPQVEQPR VVRPHATVAP  600
FDLEKTREGS GFKIFGFKVD AASASPIQLT SPMSTMREHV VQTQPPASVN ELQPVQTECL  660
PEGSVSTAGT ATENEKSIQQ APQSSKDIQS KSQGASTRSC TKVHKQGVAL GRSVDLSKFG  720
DYDELKAELD KMFEFEGELV SANKNWQIVY TDNEGDMMLV GDDPWEEFCS IVRKIYIYTK  780
EEVQKMNSKS SAPRKEEPLA SGEVCAATNE *
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-1652036117357Auxin response factor 1
4ldw_A1e-1652036117357Auxin response factor 1
4ldw_B1e-1652036117357Auxin response factor 1
4ldx_A1e-1652036117357Auxin response factor 1
4ldx_B1e-1652036117357Auxin 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.5KG746900.1.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)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP117836111
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]