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.4KG394900.1.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: 687aa    MW: 74927.4 Da    PI: 7.4423
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.4KG394900.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B3781e-24122223199
                          EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEE CS
                   B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFk 83 
                          f k+lt+sd+++ g +++p+ +ae++         ++ +  t+ ++d +g +W++++iyr++++r++lt+GW+ Fv++++L +gD++vF+
  Pavir.4KG394900.1.p 122 FAKTLTQSDANNGGGFSVPRYCAETIfprldysADPPVQ--TVLVKDVHGVVWKFRHIYRGTPRRHLLTTGWSTFVNQKKLVAGDSIVFM 209
                          89****************************996555555..8************************************************ PP

                          E-SSSEE..EEEEE-S CS
                   B3  84 ldgrsefelvvkvfrk 99 
                            +++++ l+v+++r+
  Pavir.4KG394900.1.p 210 --RTENGDLCVGIRRA 223
                          ..4588999****997 PP
2Auxin_resp113.91.5e-37279362183
           Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrl.sGtvvgvsdldpvrWpnSkWrsLk 83 
                          a++ a ++++FevvY+Prast+eF+vk+  v+ a+++++++GmRfkmafetedss++++ +Gtv++v+ +dp+rWpnS+Wr+L+
  Pavir.4KG394900.1.p 279 ASNLAVSGQPFEVVYYPRASTPEFCVKAGAVRVAMRTQWCAGMRFKMAFETEDSSRISWfMGTVSAVQVADPIRWPNSPWRLLQ 362
                          5678899***************************************************************************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.101.4E-37115227IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019362.88E-29117224IPR015300DNA-binding pseudobarrel domain
CDDcd100172.53E-21121222No hitNo description
SMARTSM010198.0E-22122224IPR003340B3 DNA binding domain
PROSITE profilePS5086313.366122224IPR003340B3 DNA binding domain
PfamPF023627.3E-23122223IPR003340B3 DNA binding domain
PfamPF065071.6E-32279362IPR010525Auxin response factor
PROSITE profilePS5174521.408600680IPR000270PB1 domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0007389Biological Processpattern specification process
GO:0009733Biological Processresponse to auxin
GO:0048829Biological Processroot cap development
GO:0051301Biological Processcell division
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0005515Molecular Functionprotein binding
Sequence ? help Back to Top
Protein Sequence    Length: 687 aa     Download sequence    Send to blast
MITFVDSAAM ERERESDRCL DPQLWHACAG GMVQMPPVHS KVYYFPQGHA EHAQGPVDLP  60
AGRVPALVLC RVAAVRFMAD PDTDEVFAKI RLAPVRPNDP GYAADADDAI GAGAQEDKPA  120
SFAKTLTQSD ANNGGGFSVP RYCAETIFPR LDYSADPPVQ TVLVKDVHGV VWKFRHIYRG  180
TPRRHLLTTG WSTFVNQKKL VAGDSIVFMR TENGDLCVGI RRAKKGGIGG PEFLHQPPPP  240
GGNYGGFSMF LRGEEDGNKM MATRGKVRVR VRPEEVVEAS NLAVSGQPFE VVYYPRASTP  300
EFCVKAGAVR VAMRTQWCAG MRFKMAFETE DSSRISWFMG TVSAVQVADP IRWPNSPWRL  360
LQVAWDEPDL LQNVKRVSPW LVELVSNMPA IHLSPFSPPR KKLCVPMYPE LPLEGQFPTP  420
MFHGSPLGRG VGPMCYFPDG TPAGIQGARH AQFGISLSDL HLNKLQSSLS VSPHGIHHLD  480
HGMQPRIAAG LIIGHQAARD DIPCLLTIGT PQNKKSDAKK APPPQLMLFG KPILTEQQIS  540
LGNAAGFPLS TPKKSTSDDN AEKTVSNSDI SSPGSNQDGT SSGGAPLCQD NKMLDLGLET  600
GHCKVFLQSE DVGRTLDLSD VGSYEELYQR LADMFGIEKA ELMSHVFYRD ASGALKHTGD  660
KPFSEFTKTA RRLTILTDTS SDSLAR*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldu_A3e-79338332388Auxin response factor 5
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.174250.0stem
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).
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00461DAPTransfer from AT4G30080Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.4KG394900.1.p
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankKJ7279650.0KJ727965.1 Zea mays clone pUT6078 ARF transcription factor (ARF21) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_004966255.10.0auxin response factor 18
RefseqXP_004966256.10.0auxin response factor 18
SwissprotQ653H70.0ARFR_ORYSJ; Auxin response factor 18
TrEMBLA0A3L6S3T80.0A0A3L6S3T8_PANMI; Auxin response factor
STRINGPavir.Da00107.1.p0.0(Panicum virgatum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP51637152
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G30080.10.0auxin response factor 16
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. Huang J,Li Z,Zhao D
    Deregulation of the OsmiR160 Target Gene OsARF18 Causes Growth and Developmental Defects with an Alteration of Auxin Signaling in Rice.
    Sci Rep, 2016. 6: p. 29938
    [PMID:27444058]