Detailed view for PF3D7_0205500

Basic information

TDR Targets ID: 3322
Plasmodium falciparum, DNA-directed RNA polymerase II 16 kDa subunit, putative

Source Database / ID: PlasmoDB / PF3D7_0205500  GeneDB / PF3D7_0205500

pI: 6.4573 | Length (AA): 132 | MW (Da): 15114 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | Predicted trans-membrane segments: ND

Pfam domains

PF03874   RNA polymerase Rpb4

Gene Ontology

Mouse over links to read term descriptions.
GO:0055029   nuclear DNA-directed RNA polymerase complex  
GO:0005575   cellular_component  
GO:0003899   DNA-directed RNA polymerase activity  
GO:0003824   catalytic activity  
GO:0000166   nucleotide binding  
GO:0044237   cellular metabolic process  
GO:0006366   transcription from RNA polymerase II promoter  
GO:0006352   transcription initiation  
GO:0006350   transcription  

Network

Metabolic Pathways

Structural information

Modbase 3D models: 1

There is 1 model calculated for this protein. More info on this model, including the model itself is available at: Modbase

Target Beg Target End Template Template Beg Template End Identity Evalue Model Score MPQS zDope
6 130 2c35 (A) 14 140 29.00 0 1 1.41 -1.2

Help me make sense of these data.

Target Beg: first modeled residue
Target End: last modeled residue
Template: template structure used for modelling (PDB accession and chain)
Template Beg: first template residue in target-template alignment
Template End: last template residue in target-template alignment
Identity: sequence identity
Evalue: E value for target-template hit
Model Score: GA341 score (>0.7 for reliable model)
MPQS: ModPipe Quality Score (>1.1 for reliable model)
zDope: zDope Score (negative for reliable model)

A more detailed description of these scores is available at the Modbase Model Evaluation Help Pages, and in the papers referenced therein.

PDB Structures:

No structure availble in the PDB for this protein

Expression

Upregulation Percent Ranking Shows this level of upregulation in
This gene ranks in the upper 80-100% group of genes. gametocyte, sporozoite, early ring, early trophozoite, late ring, late trophozoite.
Upregulation Percent Ranking Shows this level of upregulation in
This gene ranks in the upper 60-80% group of genes. early schizont.
Show/Hide expression data references
  • PlasmoDB Data on upregulation of P. falciparum genes in different life cycle stages, combined from several microarray experiments available in PlasmoDB

Orthologs

Ortholog group members (OG5_128606)
Species Accession Gene Product
Arabidopsis thaliana AT5G09920   RNA polymerase II, Rpb4, core protein
Babesia bovis BBOV_III006040   RNA polymerase Rpb4 family protein
Brugia malayi Bm1_25045   DNA-directed RNA polymerase II 16 kDa polypeptide, putative
Candida albicans CaO19.7786   similar to N terminus of S. cerevisiae RPB4 (YJL140W) RNA polymerase II fourth largest subunit.
Candida albicans CaO19.145   similar to C terminus of S. cerevisiae RPB4 (YJL140W) RNA polymerase II fourth largest subunit.
Candida albicans CaO19.146   similar to N terminus of S. cerevisiae RPB4 (YJL140W) RNA polymerase II fourth largest subunit.
Candida albicans CaO19.7785   similar to C terminus of S. cerevisiae RPB4 (YJL140W) RNA polymerase II fourth largest subunit.
Caenorhabditis elegans CELE_F43E2.2   Protein RPB-4
Cryptosporidium parvum cgd3_4320   conserved hypothetical protein
Dictyostelium discoideum DDB_G0282739   DNA-directed RNA polymerase II subunit 4
Drosophila melanogaster Dmel_CG43662   CG43662 gene product from transcript CG43662-RF
Echinococcus granulosus EgrG_000089400   DNA directed RNA polymerase II subunit
Echinococcus multilocularis EmuJ_000089400   DNA directed RNA polymerase II subunit
Homo sapiens ENSG00000144231   polymerase (RNA) II (DNA directed) polypeptide D
Loa Loa (eye worm) LOAG_07020   DNA-directed RNA polymerase II polypeptide
Mus musculus ENSMUSG00000024258   polymerase (RNA) II (DNA directed) polypeptide D
Neospora caninum NCLIV_031640   DNA-directed RNA polymerase II, putative
Oryza sativa 4328083   Os02g0116900
Plasmodium berghei PBANKA_0303200   DNA-directed RNA polymerase II 16 kDa subunit, putative
Plasmodium falciparum PF3D7_0205500 this record   DNA-directed RNA polymerase II 16 kDa subunit, putative
Plasmodium knowlesi PKNH_0415400   DNA-directed RNA polymerase I subunit, putative
Plasmodium vivax PVX_003705   DNA-directed RNA polymerase II 16 kDa subunit, putative
Plasmodium yoelii PY02525   RNA polymerase Rpb4
Saccharomyces cerevisiae YJL140W   DNA-directed RNA polymerase II subunit RPB4
Schistosoma japonicum Sjp_0061690   ko:K03012 DNA-directed RNA polymerase II subunit D, putative
Schistosoma mansoni Smp_074230   DNA-directed RNA polymerase II
Schmidtea mediterranea mk4.002007.01   DNA-directed RNA polymerase II subunit RPB4
Toxoplasma gondii TGME49_231380   DNA-directed RNA polymerase II RPB4
Theileria parva TP02_0359   DNA-directed RNA polymerase II subunit Rpb4, putative
Trichomonas vaginalis TVAG_183050   hypothetical protein

Essentiality

PF3D7_0205500 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
CELE_F43E2.2 Caenorhabditis elegans embryonic lethal wormbase
TGME49_231380 Toxoplasma gondii Probably essential sidik

Show/Hide essentiality data references
  • sidik A Genome-wide CRISPR Screen in Toxoplasma Identifies Essential Apicomplexan Genes. Sidik, Saima M., et al. "A genome-wide CRISPR screen in toxoplasma identifies essential apicomplexan genes." Cell 166.6 (2016): 1423-1435.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • plasmo Functional Profiling of a Plasmodium Genome Reveals an Abundance of Essential Genes. Bushell, Ellen, et al. "Functional profiling of a Plasmodium genome reveals an abundance of essential genes." Cell 170.2 (2017): 260-272.
  • goodall The Essential Genome of Escherichia coli K-12 (Transposon directed high-throughput mutagenesis) Goodall, Emily CA, et al. "The essential genome of Escherichia coli K-12." mBio 9.1 (2018): e02096-17.
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170

Phenotypes and Validation (curated)

We have no manually annotated phenotypes for this target. What does this mean? / Care to help?
In TDR Targets, information about phenotypes that are caused by drugs, or by genetic manipulation of cells (e.g. gene knockouts or knockdowns) is manually curated from the literature. These descriptions help to describe the potential of the target for drug development. If no information is available for this gene or if the information is incomplete, this may mean that i) the papers containing this information either appeared after the curation effort for this organism was carried out or they were inadvertently missed by curators; or that ii) the curation effort for this organism has not yet started.
 
In any case, if you have information about papers containing relevant validation data for this target, please log in using your TDR Targets username and password and send them to us using the corresponding form in this page (only visible to registered users) or contact us.

Annotated validation

No validation data for this target

Associated compounds / Druggability

Curated from literature

No chemical compounds associated to this gene

Predicted associations

By orthology with druggable targets
Non orthologous druggable targets
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets

Assayability

Assay information

  • Assay for Ribonucleic Acid Polymerase (2.7.7.6 ) Sigma-Aldrich
  • Automatic link to known assays based on EC numbers.

Reagent availability

No reagent availability information for this target.

Bibliographic References

16 literature references were collected for this gene.

If you have references for this gene, please enter them in a user comment (below) or Contact us.

User comments

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Gene identifier PF3D7_0205500 (Plasmodium falciparum), DNA-directed RNA polymerase II 16 kDa subunit, putative
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TDR Targets Development Release v6, Revision: 1335 (10.Aug.2018)
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