Detailed view for PBANKA_0203300

Basic information

TDR Targets ID: 825779
Plasmodium berghei, DNA-directed RNA polymerase II subunit RPB9, putative
Source Database / ID: 

pI: 4.9636 | Length (AA): 226 | MW (Da): 26924 | 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

PF02150   RNA polymerases M/15 Kd subunit

Gene Ontology

Mouse over links to read term descriptions.
GO:0006351   transcription, DNA-dependent  
GO:0003676   nucleic acid binding  
GO:0008270   zinc ion binding  
GO:0006379   mRNA cleavage  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 4 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
5 221 3zhe (A) 144 358 7.00 0 0.01 1.00418 -0.19
6 109 5xog (I) 6 105 38.00 0.0000000001 1 0.745577 0.89
73 117 1tfi (A) 6 50 16.00 0.0017 0.26 0.307915 0.65
116 225 3qml (D) 138 250 10.00 0 0.01 0.601026 -0.68

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

Orthologs

Ortholog group members (OG5_128243)

Species Accession Gene Product
Arabidopsis thaliana AT4G16265   RNA polymerases subunit NRP(B/D/E)9b
Arabidopsis thaliana AT3G16980   DNA-directed RNA polymerases II, IV and V subunit 9A
Babesia bovis BBOV_II007540   DNA-directed RNA polymerase 2 subunit, putative
Brugia malayi Bm1_52995   DNA-directed RNA polymerase II 15.1 kDa polypeptide, putative
Candida albicans CaO19.9816   similar to S. cerevisiae RPB9 (YGL070C) RNA polymerase II core subunit
Candida albicans CaO19.2276   similar to S. cerevisiae RPB9 (YGL070C) RNA polymerase II core subunit
Caenorhabditis elegans CELE_Y97E10AR.5   Protein RPB-9
Cryptosporidium hominis Chro.30221   DNA-directed RNA polymerase 2 subunit
Cryptosporidium parvum cgd3_1870   DNA-directed RNA polymerase 2 subunit
Dictyostelium discoideum DDB_G0268306   RNA polymerase II core subunit
Drosophila melanogaster Dmel_CG3284   RNA polymerase II 15kD subunit
Echinococcus granulosus EgrG_000372700   RNA polymerase II 15 kDa subunit
Entamoeba histolytica EHI_056690   DNA-directed RNA polymerase II subunit, putative
Echinococcus multilocularis EmuJ_000372700   RNA polymerase II 15 kDa subunit
Homo sapiens ENSG00000105258   polymerase (RNA) II (DNA directed) polypeptide I, 14.5kDa
Leishmania braziliensis LbrM.28.0130   DNA-direcetd RNA polymerase II, subunit 9, putative
Leishmania donovani LdBPK_280120.1   DNA-direcetd RNA polymerase II, subunit 9, putative
Leishmania infantum LinJ.28.0120   DNA-direcetd RNA polymerase II, subunit 9, putative
Leishmania major LmjF.28.0120   DNA-direcetd RNA polymerase II, subunit 9, putative
Leishmania mexicana LmxM.28.0120   DNA-direcetd RNA polymerase II, subunit 9, putative
Loa Loa (eye worm) LOAG_00779   hypothetical protein
Mus musculus ENSMUSG00000019738   polymerase (RNA) II (DNA directed) polypeptide I
Neospora caninum NCLIV_022210   hypothetical protein
Oryza sativa 4331295   Os03g0102200
Oryza sativa 4352511   Os12g0560400
Oryza sativa 4343902   Os07g0615800
Plasmodium berghei PBANKA_0203300   DNA-directed RNA polymerase II subunit RPB9, putative
Plasmodium falciparum PF3D7_0110400   DNA-directed RNA polymerase II subunit RPB9, putative
Plasmodium knowlesi PKNH_0203500   DNA-directed RNA polymerase II subunit RPB9, putative
Plasmodium vivax PVX_081277   DNA-directed RNA polymerase 2, putative
Plasmodium vivax PVX_136260   unspecified product
Plasmodium yoelii PY00422   DNA-directed RNA polymerase ii 15.1 kDa polypeptide
Saccharomyces cerevisiae YGL070C   DNA-directed RNA polymerase II core subunit RPB9
Schistosoma japonicum Sjp_0089430   ko:K03017 DNA-directed RNA polymerase II subunit I, putative
Schistosoma mansoni Smp_067090   DNA-directed RNA polymerase II
Schmidtea mediterranea mk4.001708.02   DNA-directed RNA polymerase II subunit RPB9
Schmidtea mediterranea mk4.025637.00  
Schmidtea mediterranea mk4.001721.00  
Trypanosoma brucei gambiense Tbg972.11.8320   DNA-direcetd RNA polymerase II, subunit 9, putative
Trypanosoma brucei Tb11.v5.0255   DNA-directed RNA polymerase II, subunit 9, putative
Trypanosoma cruzi TcCLB.511153.130   DNA-direcetd RNA polymerase II, subunit 9, putative
Trypanosoma cruzi TcCLB.506779.60   DNA-direcetd RNA polymerase II, subunit 9, putative
Toxoplasma gondii TGME49_202690   DNA-directed RNA polymerase II RPB9
Theileria parva TP02_0205   DNA-directed RNA polymerase II subunit, putative
Trichomonas vaginalis TVAG_212550   conserved hypothetical protein

Essentiality

PBANKA_0203300 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb11.02.5180 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb11.02.5180 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb11.02.5180 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb11.02.5180 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
PBANKA_0203300 this record Plasmodium berghei Slow plasmo
TGME49_202690 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.
  • 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.

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User comments

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Gene identifier PBANKA_0203300 (Plasmodium berghei), DNA-directed RNA polymerase II subunit RPB9, putative
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