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.6NG358100.3.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 C2H2
Protein Properties Length: 526aa    MW: 54325.7 Da    PI: 9.579
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.6NG358100.3.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H217.41.2e-056082123
                         EEETTTTEEESSHHHHHHHHHHT CS
              zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                         ++C+ C+k F r  nL+ H r H
  Pavir.6NG358100.3.p 60 FVCEVCNKGFQREQNLQLHRRGH 82
                         89*******************88 PP
2zf-C2H213.30.00026136158123
                          EEETTTTEEESSHHHHHHHHHHT CS
              zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                          +kC +C+k++  +s+ k H +t+
  Pavir.6NG358100.3.p 136 WKCDKCNKRYAVQSDWKAHSKTC 158
                          58*****************9998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576671.38E-75982No hitNo description
Gene3DG3DSA:3.30.160.607.1E-65982IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.0946082IPR007087Zinc finger, C2H2
SMARTSM003550.00416082IPR015880Zinc finger, C2H2-like
PfamPF121713.4E-56082IPR022755Zinc finger, double-stranded RNA binding
PROSITE patternPS0002806282IPR007087Zinc finger, C2H2
SMARTSM00355300101131IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.603.8E-5124157IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576671.38E-7131156No hitNo description
SMARTSM00355110136156IPR015880Zinc 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: 526 aa     Download sequence    Send to blast
MAAAHLFGLG DAQMQPPLPQ QAAPPPPAAA PAPKKKRNQP DPDAEVIALS PKSLLATNRF  60
VCEVCNKGFQ REQNLQLHRR GHNLPWKLKQ KNPKETRRRV YLCPEPTCVH HDPSRALGDL  120
TGIKKHYCRK HGEKKWKCDK CNKRYAVQSD WKAHSKTCGT REYRCDCGTL FSRRDSFITH  180
RAFCDAMAQE SARAPPIGAG MYGSGGMALG LSGLAASQLH SFQDQAHSSA ATAIGGNPAA  240
QFEHLMPSSA GSPAFRGAQP ASSSSSPFYL GGAEDGHQSQ PGHTSLLHGK PAFHGLMQLP  300
EQHGQPGSNG LLNLGFFSGA SSGQDARLVF PNQFNGATGG NGRGDGSEHG NSGANTGSAA  360
IFSGNLMGNQ MAGGGGGFSS SLYNSTETVA PPQMSATALL QKAAQMGATT SGGGGGSVNS  420
LLRGLGSGGA LNGRPSGAAG FMAGESSSSR STSQAENESQ FRDLMNSLAA SGSGGFPGMD  480
DGKLSTRDFL GVSGGVVRSM GGAAGLPLRH GAAGIGMGSL DPEMK*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C1e-33132193364Zinc finger protein JACKDAW
5b3h_F1e-33132193364Zinc finger protein JACKDAW
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.45240.0callus| leaf| root| stem
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Highly expressed in leaf tissues. {ECO:0000305|PubMed:22898356}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor acting as a positive regulator of the starch synthase SS4. Controls chloroplast development and starch granule formation (PubMed:22898356). 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:22898356, ECO:0000269|PubMed:24821766}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00255DAPTransfer from AT2G02070Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.6NG358100.3.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
GenBankBT0538220.0BT053822.1 Zea mays full-length cDNA clone ZM_BFb0209O02 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025821062.10.0protein indeterminate-domain 5, chloroplastic-like isoform X2
SwissprotQ9ZUL31e-120IDD5_ARATH; Protein indeterminate-domain 5, chloroplastic
TrEMBLA0A3L6PM370.0A0A3L6PM37_PANMI; INDETERMINATE-related protein 1
STRINGPavir.Fb02381.1.p0.0(Panicum virgatum)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G02080.11e-107indeterminate(ID)-domain 4
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]