Detailed view for PBANKA_1021900

Basic information

TDR Targets ID: 828911
Plasmodium berghei, DNA-directed RNA polymerase III subunit RPC6, putative
Source Database / ID: 

pI: 9.2423 | Length (AA): 287 | MW (Da): 34112 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | Predicted trans-membrane segments: 0

Druggability Group : DG

Targets have been classified into druggability groups (DG) according to their druggability score in network driven prioritizations. DGs range from 1 to 5; the higher the group number, the higher the chance of the target to be druggable

Pfam domains

PF05158   RNA polymerase Rpc34 subunit

Gene Ontology

Mouse over links to read term descriptions.
GO:0005666   DNA-directed RNA polymerase III complex  
GO:0006383   transcription from RNA polymerase III promoter  

Metabolic Pathways

Purine metabolism (KEGG)
Pyrimidine metabolism (KEGG)
RNA polymerase (KEGG)

Structural information

Modbase 3D models:

There are 3 models calculated for this protein. More info on these models, including the models themselves is available at: Modbase

Target Beg Target End Template Template Beg Template End Identity Evalue Model Score MPQS zDope
1 250 1j7n (A) 265 557 18.00 0 0.94 0.83918 1.39
7 78 2dk8 (A) 14 80 10.00 0.0000053 0.36 0.390771 -0.81
166 278 5gyj (A) 45 153 32.00 0.057 0.17 0.489928 1.03

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 Stage Dataset
Upper 80-100% percentile Ookinete. Otto TD
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile 4 hs Ring. Otto TD
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile Gametocyte, 16 hs Trophozoite, 22 hs Schizont, Erthyrocytic stages, Male gametocyte. Otto TD Yeoh LM
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile Female gametocyte. Yeoh LM
Show/Hide expression data references
  • Otto TD A comprehensive evaluation of rodent malaria parasite genomes and gene expression.
  • Yeoh LM Comparative transcriptomics of female and male gametocytes in Plasmodium berghei and the evolution of sex in alveolates.

Orthologs

Ortholog group members (OG5_128634)

Species Accession Gene Product
Arabidopsis thaliana AT5G23710   DNA binding / DNA-directed RNA polymerase
Babesia bovis BBOV_IV011150   RNA polymerase rpc34 subunit containing protein
Brugia malayi Bm1_47790   RNA polymerase Rpc34 subunit family protein
Candida albicans CaO19.13051   RNA polymerase III
Candida albicans CaO19.5608   RNA polymerase III
Caenorhabditis elegans CELE_W09C3.4   Protein W09C3.4
Cryptosporidium hominis Chro.60525   DNA-directed RNA polymerases iii 39 Kd polypeptide
Cryptosporidium parvum cgd6_4580   RNA polymerase III C34 subunit; rpc34p ortholog
Dictyostelium discoideum DDB_G0272022   RNA polymerase III subunit
Drosophila melanogaster Dmel_CG5380   CG5380 gene product from transcript CG5380-RB
Echinococcus granulosus EgrG_000214900   DNA directed RNA polymerase III subunit RPC6
Entamoeba histolytica EHI_147230   hypothetical protein
Echinococcus multilocularis EmuJ_000214900   DNA directed RNA polymerase III subunit RPC6
Homo sapiens ENSG00000132664   polymerase (RNA) III (DNA directed) polypeptide F, 39 kDa
Loa Loa (eye worm) LOAG_08512   RNA polymerase Rpc34 subunit family protein
Mus musculus ENSMUSG00000027427   polymerase (RNA) III (DNA directed) polypeptide F
Neospora caninum NCLIV_062360   DNA-directed RNA polymerases III, 39 kDa polypeptide, putative
Oryza sativa 4341464   Os06g0603400
Plasmodium berghei PBANKA_1021900   DNA-directed RNA polymerase III subunit RPC6, putative
Plasmodium falciparum PF3D7_1421400   DNA-directed RNA polymerase III subunit RPC6, putative
Plasmodium knowlesi PKNH_1336500   DNA-directed RNA polymerase III subunit RPC6, putative
Plasmodium yoelii PY07258   probable DNA-directed RNA polymerase iii 34 kDa polypeptide
Saccharomyces cerevisiae YNR003C   Rpc34p
Schistosoma japonicum Sjp_0134920   ko:K03025 DNA-directed RNA polymerase III subunit C34, putative
Schistosoma mansoni Smp_165980   rna polymerase III (DNA directed) 39kD subunit-related
Toxoplasma gondii TGME49_217580   DNA-directed RNA polymerase III RPC6
Theileria parva TP01_0652   RNA polymerase subunit, putative
Trichomonas vaginalis TVAG_074910   conserved hypothetical protein

Essentiality

PBANKA_1021900 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
YNR003C Saccharomyces cerevisiae inviable yeastgenome
PBANKA_1021900 this record Plasmodium berghei Essential plasmo
TGME49_217580 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930

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 contact us.

Annotated validation

No validation data for this target

Associated compounds / Druggability

Known modulators for this target

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
Obtained from network model
No druggable targets predicted through repurposing network model

Assayability

Assay information

No assay information for this target.

Reagent availability

No reagent availability information for this target.

Bibliographic References

No literature references available for this target.

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 PBANKA_1021900 (Plasmodium berghei), DNA-directed RNA polymerase III subunit RPC6, putative
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