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.5NG260900.5.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 C2H2
Protein Properties Length: 395aa    MW: 41892.5 Da    PI: 9.6452
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.5NG260900.5.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H217.98.8e-0690112123
                          EEETTTTEEESSHHHHHHHHHHT CS
              zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                          ++C+ C+k F r  nL+ H r H
  Pavir.5NG260900.5.p  90 FVCEVCNKGFQREQNLQLHRRGH 112
                          89*******************88 PP
2zf-C2H212.30.00051167189123
                          EEETTTTEEESSHHHHHHHHHHT CS
              zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                          +kC +C+k++  +s+ k H +++
  Pavir.5NG260900.5.p 167 WKCDKCSKRYAVQSDWKAHSKVC 189
                          58*****************9877 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.30.160.605.0E-689112IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576671.37E-789112No hitNo description
PROSITE profilePS5015711.09490112IPR007087Zinc finger, C2H2
SMARTSM003550.004190112IPR015880Zinc finger, C2H2-like
PfamPF121712.4E-590112IPR022755Zinc finger, double-stranded RNA binding
PROSITE patternPS00028092112IPR007087Zinc finger, C2H2
SMARTSM00355290132162IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.602.9E-4155187IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576671.37E-7162187No hitNo description
SMARTSM00355140167187IPR015880Zinc finger, C2H2-like
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0003676Molecular Functionnucleic acid binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 395 aa     Download sequence    Send to blast
MASNSSAAAV AALFGIRDGD HQEQIKPLLA QPHQQLPPAP LLSAAASSSA PGSAQAAAAS  60
PPVKKKRTLP DPDAEVIALS PKTLLATNRF VCEVCNKGFQ REQNLQLHRR GHNLPWKLKQ  120
KDPLQAQRRR VYLCPEPTCA HHDPSRALGD LTGIKKHFCR KHGEKKWKCD KCSKRYAVQS  180
DWKAHSKVCG TREYRCDCGT LFSRRDSFIT HRAFCDALAQ ESARLPPPGL TASHLYGATT  240
AANMALSLSQ VGSHLASTLG GDAHGHHYHQ ADLLRHGAAN RFDHHLLGPS SASAFRPLPP  300
PPSSAFLMGA PHEFIDGGDG TGSHAFLQGK AFQGLMHLPD LQGNGAGGGP LASSAPGLFN  360
LGYIASSANS SAAEGALPAV TTRLLLAGCT TTRP*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C7e-35163225365Zinc finger protein JACKDAW
5b3h_F7e-35163225365Zinc finger protein JACKDAW
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.45241e-165callus| leaf| root| stem
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor that may act a transcriptional activator of nuclear-encoded photosynthetic gene expression (Probable). Binds DNA via its zinc fingers (PubMed:24821766). Recognizes and binds to SCL3 promoter sequence 5'-AGACAA-3' to promotes its expression when in complex with RGA (PubMed:24821766). {ECO:0000269|PubMed:24821766, ECO:0000305|PubMed:19726569}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.5NG260900.5.p
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Down-regulated by gibberellin. {ECO:0000305|PubMed:17933900}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankBT0542580.0BT054258.1 Zea mays full-length cDNA clone ZM_BFb0200O05 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_004953416.10.0protein indeterminate-domain 4, chloroplastic
RefseqXP_022681782.10.0protein indeterminate-domain 4, chloroplastic
RefseqXP_022681786.10.0protein indeterminate-domain 4, chloroplastic
SwissprotQ8GYC11e-103IDD4_ARATH; Protein indeterminate-domain 4, chloroplastic
TrEMBLA0A1E5V9G20.0A0A1E5V9G2_9POAL; Protein indeterminate-domain 6, chloroplastic
STRINGPavir.J10227.1.p0.0(Panicum virgatum)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G02670.11e-103indeterminate(ID)-domain 12
Publications ? help Back to Top
  1. Moreno-Risueno MA, et al.
    Transcriptional control of tissue formation throughout root development.
    Science, 2015. 350(6259): p. 426-30
    [PMID:26494755]