Detailed view for PBANKA_1135600

Basic information

TDR Targets ID: 828206
Plasmodium berghei, exosome complex exonuclease RRP44, putative
Source Database / ID: 

pI: 7.45 | Length (AA): 1017 | MW (Da): 119421 | 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

PF00773   RNB domain
PF13638   PIN domain
PF17215   S1 domain

Gene Ontology

Mouse over links to read term descriptions.
No GO information for this protein.

Metabolic Pathways

RNA degradation (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
15 1016 5c0w (J) 20 1001 30.00 0 1 1.17925 0.52
16 999 5c0w (J) 21 984 33.00 0 1 1.13865 0.83
65 193 2hww (B) 1247 1409 13.00 0.00042 1 0.348844 -1.16

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 60-80% percentile 16 hs Trophozoite, Erthyrocytic stages. Otto TD Yeoh LM
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile 4 hs Ring, Female gametocyte. Otto TD Yeoh LM
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile Ookinete, Male gametocyte. Otto TD Yeoh LM
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile Gametocyte, 22 hs Schizont. Otto TD
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_127058)

Species Accession Gene Product
Arabidopsis thaliana AT2G17510   ribonuclease II family protein
Babesia bovis BBOV_I003540   RNB-like domain containing protein
Brugia malayi Bm1_17655   RNB-like protein
Candida albicans CaO19.12694   similar to S. cerevisiae DIS3 (YOL021C) exosome component involved mRNA degradation and nuclear RNA processing
Candida albicans CaO19.5229   similar to S. cerevisiae DIS3 (YOL021C) exosome component involved mRNA degradation and nuclear RNA processing
Caenorhabditis elegans CELE_C04G2.6   Protein DIS-3
Cryptosporidium hominis Chro.20227   mitotic control protein dis3
Cryptosporidium parvum cgd2_2090   mitotic control protein dis3, putative
Chlamydia trachomatis CT_397   ribonuclease R
Dictyostelium discoideum DDB_G0293614   hypothetical protein
Dictyostelium discoideum DDB_G0268186   hypothetical protein
Drosophila melanogaster Dmel_CG6413   CG6413 gene product from transcript CG6413-RA
Escherichia coli b4179   exoribonuclease R, RNase R
Echinococcus granulosus EgrG_000518000   dis3 exonuclease 1
Entamoeba histolytica EHI_160720   exosome complex exonuclease, putative
Echinococcus multilocularis EmuJ_000518000   dis3 exonuclease 1
Giardia lamblia GL50803_112718   Mitotic control protein dis3
Homo sapiens ENSG00000166938   DIS3 like exosome 3'-5' exoribonuclease
Homo sapiens ENSG00000083520   DIS3 exosome endoribonuclease and 3'-5' exoribonuclease
Leishmania braziliensis LbrM.28.0340   rrp44p homologue, putative
Leishmania donovani LdBPK_280470.1   rrp44p homologue, putative
Leishmania infantum LinJ.28.0470   rrp44p homologue, putative
Leishmania major LmjF.28.0330   rrp44p homologue, putative
Leishmania mexicana LmxM.28.0330   rrp44p homologue, putative
Loa Loa (eye worm) LOAG_02690   hypothetical protein
Mus musculus ENSMUSG00000032396   DIS3 mitotic control homolog (S. cerevisiae)-like
Mus musculus ENSMUSG00000033166   DIS3 mitotic control homolog (S. cerevisiae)
Neospora caninum NCLIV_026230   DIS3-like exonuclease 1 (EC 3.1.13.-), related
Oryza sativa 4331494   Os03g0129200
Plasmodium berghei PBANKA_1135600   exosome complex exonuclease RRP44, putative
Plasmodium falciparum PF3D7_1359300   exosome complex exonuclease RRP44
Plasmodium knowlesi PKNH_1112000   exosome complex exonuclease RRP44, putative
Plasmodium vivax PVX_114935   exosome complex exonuclease RRP44, putative
Plasmodium yoelii PY02885   hypothetical protein
Plasmodium yoelii PY06658   probable mitotic control protein dis3
Saccharomyces cerevisiae YOL021C   exosome catalytic subunit DIS3
Schistosoma japonicum Sjp_0071900   DIS3-like exonuclease 1, putative
Schistosoma japonicum Sjp_0071890   ko:K01149 DIS3 mitotic control homolog [EC:3.1.13.-], putative
Schistosoma mansoni Smp_161980   ribonuclease II-related
Schmidtea mediterranea mk4.001720.00   DIS3-like exonuclease 1
Schmidtea mediterranea mk4.031335.00  
Schmidtea mediterranea mk4.037021.03  
Schmidtea mediterranea mk4.054278.02  
Schmidtea mediterranea mk4.031335.01  
Trypanosoma brucei gambiense Tbg972.11.8560   exosome complex exonuclease RRP44p homologue, putative
Trypanosoma brucei Tb11.02.5380   exosome complex exonuclease RRP44p homologue
Trypanosoma cruzi TcCLB.508241.120   rrp44p homologue, putative
Toxoplasma gondii TGME49_261050   RNB family domain-containing protein
Theileria parva TP01_0496   mitotic control protein dis3, putative
Trichomonas vaginalis TVAG_311220   ribonuclease, putative

Essentiality

PBANKA_1135600 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb11.02.5380 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb11.02.5380 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb11.02.5380 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb11.02.5380 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
b4179 Escherichia coli non-essential goodall
CELE_C04G2.6 Caenorhabditis elegans slow growth wormbase
YOL021C Saccharomyces cerevisiae inviable yeastgenome
PBANKA_1135600 this record Plasmodium berghei Essential plasmo
TGME49_261050 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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.
  • 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
  • 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.
  • 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
  • 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.

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

No user comments are available for this gene. Log in to add comments, or register.

Enter your comment

User ()
Gene identifier PBANKA_1135600 (Plasmodium berghei), exosome complex exonuclease RRP44, putative
Title for this comment
Comment