Detailed view for PF3D7_1104700

Basic information

TDR Targets ID: 1537
Plasmodium falciparum, DNA-directed RNA polymerase III subunit RPC8, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 4.9781 | Length (AA): 184 | MW (Da): 21621 | Paralog Number: 0

Signal peptide: Y | 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

PF03876   SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397
PF08292   RNA polymerase III subunit Rpc25

Gene Ontology

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

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 7 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
43 233 2ckz (B) 1 212 32.00 0 1 1.2 -0.59
1 186 2ckz (B) 1 212 33.00 0 1 1.3794 -0.1
1 186 3ayh (B) 1 203 32.00 0 1 1.3354 -0.06
1 186 1go3 (E) 1 177 22.00 0 1 1.179 0.41
1 184 2ckz (B) 1 212 33.00 0 1 1.3638 -0.02
1 184 3ayh (B) 1 203 32.00 0 1 1.3218 0
1 184 1go3 (E) 1 177 22.00 0 1 1.1925 0.33

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

Orthologs

Ortholog group members (OG5_127589)

Species Accession Gene Product
Arabidopsis thaliana AT1G06790   RNA polymerase Rpb7 N-terminal domain-containing protein
Babesia bovis BBOV_III006170   conserved hypothetical protein
Brugia malayi Bm1_54365   RNA polymerase Rpb7, N-terminal domain containing protein
Candida albicans CaO19.8073   RNA polymerase 3 subunit
Candida albicans CaO19.443   RNA polymerase 3 subunit
Caenorhabditis elegans CELE_ZK856.10   Protein RPC-25
Cryptosporidium hominis Chro.10225   hypothetical protein
Cryptosporidium parvum cgd1_1960   RPB7 subunit of the RNA polymerase III, OB fold
Dictyostelium discoideum DDB_G0273425   RNA polymerase III subunit
Dictyostelium discoideum DDB_G0273523   RNA polymerase III subunit
Drosophila melanogaster Dmel_CG7339   CG7339 gene product from transcript CG7339-RB
Echinococcus granulosus EgrG_000678100   DNA directed RNA polymerase III subunit
Entamoeba histolytica EHI_050830   DNA-directed RNA polymerase III subunit, putative
Echinococcus multilocularis EmuJ_000678100   DNA directed RNA polymerase III subunit
Giardia lamblia GL50803_3974   DNA-directed RNA polymerase III subunit 22.9 kDa polypeptide
Homo sapiens ENSG00000100413   polymerase (RNA) III (DNA directed) polypeptide H (22.9kD)
Leishmania braziliensis LbrM.09.1120   DNA-directed RNA polymerase III subunit, putative
Leishmania donovani LdBPK_091120.1   DNA-directed RNA polymerase III subunit, putative
Leishmania infantum LinJ.09.1120   DNA-directed RNA polymerase III subunit, putative
Leishmania major LmjF.09.1060   DNA-directed RNA polymerase III subunit, putative
Leishmania mexicana LmxM.09.1060   DNA-directed RNA polymerase III subunit, putative
Loa Loa (eye worm) LOAG_05614   RNA polymerase Rpb7 domain-containing protein
Mus musculus ENSMUSG00000022476   polymerase (RNA) III (DNA directed) polypeptide H
Neospora caninum NCLIV_043800   hypothetical protein
Oryza sativa 4343220   Os07g0477000
Oryza sativa 9266139   Os08g0290900
Onchocerca volvulus OVOC13497  
Plasmodium berghei PBANKA_0942200   DNA-directed RNA polymerase III subunit RPC8, putative
Plasmodium falciparum PF3D7_1104700   DNA-directed RNA polymerase III subunit RPC8, putative
Plasmodium knowlesi PKNH_0902300   DNA-directed RNA polymerase III subunit RPC8, putative
Plasmodium vivax PVX_090915   RNA polymerase Rpb7, N-terminal domain containing protein
Plasmodium yoelii PY02385   RNA polymerase Rpb7, N-terminal domain, putative
Saccharomyces cerevisiae YKL144C   DNA-directed RNA polymerase III subunit RPC25
Schistosoma japonicum Sjp_0212400   ko:K03022 DNA-directed RNA polymerase III subunit C25, putative
Schistosoma mansoni Smp_174370   DNA-directed rna polymerase III 25 kD polypeptide
Schmidtea mediterranea mk4.000039.00   DNA-directed RNA polymerase III subunit RPC8
Trypanosoma brucei gambiense Tbg972.11.14780   RNA polymerase subunit, putative
Trypanosoma brucei Tb927.11.13240   RNA polymerase subunit, putative
Trypanosoma congolense TcIL3000.11.13600   RNA polymerase subunit, putative
Trypanosoma cruzi TcCLB.510359.320   DNA-directed RNA polymerase III subunit, putative
Trypanosoma cruzi TcCLB.503819.20   DNA-directed RNA polymerase III subunit, putative
Toxoplasma gondii TGME49_292300   DNA-directed RNA polymerase III RPC8
Toxoplasma gondii TGME49_292310   RNA polymerase Rpb7, N-terminal domain-containing protein
Theileria parva TP02_0345   hypothetical protein
Trichomonas vaginalis TVAG_200150   DNA-directed RNA polymerase II, III, putative

Essentiality

PF3D7_1104700 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb11.01.4820 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb11.01.4820 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb11.01.4820 Trypanosoma brucei significant gain of fitness in procyclic forms alsford
Tb11.01.4820 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_ZK856.10 Caenorhabditis elegans larval arrest wormbase
CELE_ZK856.10 Caenorhabditis elegans slow growth wormbase
CELE_ZK856.10 Caenorhabditis elegans sterile wormbase
YKL144C Saccharomyces cerevisiae inviable yeastgenome
TGME49_292300 Toxoplasma gondii Essentiality uncertain sidik
TGME49_292310 Toxoplasma gondii Essentiality uncertain sidik
TGME49_292300 Toxoplasma gondii Probably essential sidik
TGME49_292310 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84

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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Gene identifier PF3D7_1104700 (Plasmodium falciparum), DNA-directed RNA polymerase III subunit RPC8, putative
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