Detailed view for PF3D7_1342700

Basic information

TDR Targets ID: 124
Plasmodium falciparum, DNA-directed RNA polymerases I, II, and III subunit RPABC4, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 8.1105 | Length (AA): 58 | MW (Da): 6746 | Paralog Number: 0

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

Druggability Group : DG1

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

PF03604   DNA directed RNA polymerase, 7 kDa subunit

Gene Ontology

Mouse over links to read term descriptions.
GO:0006351   transcription, DNA-dependent  
GO:0003899   DNA-directed RNA polymerase activity  
GO:0003700   transcription factor activity  
GO:0003677   DNA binding  
GO:0006350   transcription  

Metabolic Pathways

Purine metabolism (KEGG)
Pyrimidine metabolism (KEGG)
Global map (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
14 58 1twf (L) 26 70 40.00 0 0.84 1.09 0.71
5 40 3pwf (A) 129 161 42.00 0.38 0.82 1.00689 0.12
13 58 1twf (L) 25 70 39.00 0 0.99 1.1529 1.2
14 50 2lcq (A) 126 161 33.00 0.005 0.76 0.968131 0.42

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 gametocyte, sporozoite, early ring, early trophozoite, late ring, Oocyst, Ring, Sporozoite, Female Gametocyte, Male Gametocyte. PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 8 hs, intra-erythrocytic - 24 hs, intra-erythrocytic - 32 hs, late trophozoite. Otto TD PlasmoDB
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 16 hs, intra-erythrocytic - 48 hs. Otto TD
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intra-erythrocytic - 0 hs. Otto TD
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile intra-erythrocytic - 40 hs. Otto TD
Show/Hide expression data references
  • Lasonder E Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes. Molecular insight into sex-specific processes and translational repression.
  • Otto TD New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.
  • PlasmoDB Data on upregulation of P. falciparum genes in different life cycle stages, combined from several microarray experiments available in PlasmoDB
  • Zanghi G A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection.

Orthologs

Ortholog group members (OG5_130124)

Species Accession Gene Product
Arabidopsis thaliana AT5G41010   DNA-directed RNA polymerase NRPB12/NRPD12/NRPE12
Candida albicans CaO19.7255   DNA-directed RNA polymerase
Caenorhabditis elegans CELE_F23B2.13   Protein RPB-12
Cryptosporidium parvum cgd7_3240   transcription activator, putative
Dictyostelium discoideum DDB_G0283365   RNA polymerase I core subunit
Drosophila melanogaster Dmel_CG34186   CG34186 gene product from transcript CG34186-RA
Echinococcus granulosus EgrG_000657300   dna directed rna polymerases i ii and iii
Echinococcus multilocularis EmuJ_000657300   DNA directed RNA polymerases I, II, and III
Homo sapiens ENSG00000147669   polymerase (RNA) II (DNA directed) polypeptide K, 7.0kDa
Loa Loa (eye worm) LOAG_10524   hypothetical protein
Mus musculus ENSMUSG00000045996   polymerase (RNA) II (DNA directed) polypeptide K
Mus musculus 100862456   DNA-directed RNA polymerases I, II, and III subunit RPABC4-like
Mus musculus 102641086   DNA-directed RNA polymerases I, II, and III subunit RPABC4-like
Oryza sativa 9269422   Os01g0530366
Oryza sativa 9272152   Os05g0151800
Oryza sativa 9266234   Os07g0105100
Plasmodium berghei PBANKA_1355800   DNA-directed RNA polymerases I, II, and III subunit RPABC4, putative
Plasmodium falciparum PF3D7_1342700   DNA-directed RNA polymerases I, II, and III subunit RPABC4, putative
Plasmodium knowlesi PKNH_1258700   DNA-directed RNA polymerases I, II, and III subunit RPABC4, putative
Plasmodium vivax PVX_083032   transcription activator, putative
Saccharomyces cerevisiae YHR143W-A   DNA-directed RNA polymerase core subunit RPB12
Schistosoma japonicum Sjp_0308900   ko:K03009 DNA-directed RNA Polymerase II subunit K, putative
Schistosoma mansoni Smp_132030   hypothetical protein
Schmidtea mediterranea mk4.004777.01  
Toxoplasma gondii TGME49_254140   DNA-directed RNA polymerase II RPABC4
Trichomonas vaginalis TVAG_040880   conserved hypothetical protein

Essentiality

PF3D7_1342700 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
CELE_F23B2.13 Caenorhabditis elegans embryonic lethal wormbase
CELE_F23B2.13 Caenorhabditis elegans larval arrest wormbase
CELE_F23B2.13 Caenorhabditis elegans sterile wormbase
YHR143W-A Saccharomyces cerevisiae inviable yeastgenome
PBANKA_1355800 Plasmodium berghei Essential plasmo
TGME49_254140 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
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • 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
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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.

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 PF3D7_1342700 (Plasmodium falciparum), DNA-directed RNA polymerases I, II, and III subunit RPABC4, putative
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