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.6KG404500.1.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 C2H2
Protein Properties Length: 533aa    MW: 55088.6 Da    PI: 9.3221
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.6KG404500.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H217.41.3e-056486123
                         EEETTTTEEESSHHHHHHHHHHT CS
              zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                         ++C+ C+k F r  nL+ H r H
  Pavir.6KG404500.1.p 64 FVCEVCNKGFQREQNLQLHRRGH 86
                         89*******************88 PP
2zf-C2H213.20.00026140162123
                          EEETTTTEEESSHHHHHHHHHHT CS
              zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                          +kC +C+k++  +s+ k H +t+
  Pavir.6KG404500.1.p 140 WKCDKCNKRYAVQSDWKAHSKTC 162
                          58*****************9998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576671.83E-76386No hitNo description
Gene3DG3DSA:3.30.160.607.2E-66386IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.00416486IPR015880Zinc finger, C2H2-like
PfamPF121713.4E-56486IPR022755Zinc finger, double-stranded RNA binding
PROSITE profilePS5015711.0946486IPR007087Zinc finger, C2H2
PROSITE patternPS0002806686IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.603.9E-5128161IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576671.83E-7135160No hitNo description
SMARTSM00355110140160IPR015880Zinc 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: 533 aa     Download sequence    Send to blast
MAAAHLFGLG DAQTMQPPLP QQAAPPPPAA APALKKKRNQ PGNPNPDAEV IALSPKTLLA  60
TNRFVCEVCN KGFQREQNLQ LHRRGHNLPW KLKQKNPKET RRRVYLCPEP SCVHHDPSRA  120
LGDLTGIKKH YCRKHGEKKW KCDKCNKRYA VQSDWKAHSK TCGTREYRCD CGTLFSRRDS  180
FITHRAFCDA LAQESARAPP IGAGMYGSGG MALGLSGLAA SQLHSFQDQQ AHSSAATAIT  240
GNPAAQFEHL MPSSAGSPAF RGAQPASSSS SPFYLGGAED GHQSQPGHTS LLHGKPAFHG  300
LMQLPEQHGQ PGSNGLLNLG FFSGASSGQD ARLVFPDQFN GAAGGNGRGD GGEHGNSGAN  360
TESAAIFSGN NLMGNQMGVG GGGGFSSSLY NSTETVAPPQ MSATALLQKA AQMGATTSGA  420
GGGSVNSLLR GLGSGGALNG RPAGAAGFMA GESSSSRSTC QAENESQFRD LMNSLAASGS  480
GGFPGMDDGK LSTRDFLGVG GGVVRSMGGA VGLPLRHGAA GIGMGSLDPE MK*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C4e-34136197364Zinc finger protein JACKDAW
5b3h_F4e-34136197364Zinc 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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.6KG404500.1.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_025821061.10.0protein indeterminate-domain 5, chloroplastic-like isoform X1
SwissprotQ9ZUL31e-123IDD5_ARATH; Protein indeterminate-domain 5, chloroplastic
TrEMBLA0A3L6PM370.0A0A3L6PM37_PANMI; INDETERMINATE-related protein 1
STRINGPavir.Fa00016.1.p0.0(Panicum virgatum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP20238320
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G14580.21e-113C2H2-like zinc finger protein
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]