Detailed view for TGME49_203610

Basic information

TDR Targets ID: 264655
Toxoplasma gondii, 3'-5' exoribonuclease csl4, putative
Source Database / ID:  ToxoDB 

pI: 8.8254 | Length (AA): 269 | MW (Da): 28395 | 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

PF10447   Exosome component EXOSC1/CSL4
PF14382   Exosome complex exonuclease RRP4 N-terminal region

Gene Ontology

Mouse over links to read term descriptions.
GO:0000178   exosome (RNase complex)  
GO:0003723   RNA binding  

Metabolic Pathways

RNA degradation (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
58 265 4ifd (I) 1 291 38.00 0 1 0.991134 0.26
58 265 4ifd (I) 13 291 37.00 0 1 1.00183 0.52
63 231 4ifd (H) 50 194 28.00 0.0025 1 0.695553 0.74
65 251 2ba0 (A) 2 149 23.00 0 1 0.674767 0.71
66 262 2nn6 (I) 6 185 37.00 0 0.98 0.978242 1.16
143 225 3aev (A) 9 84 24.00 0.0072 0.71 0.53745 -0.44
143 228 3bzc (A) 652 728 23.00 0.00021 0.76 0.478603 0.01

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 VEG Tachyzoite, ME49 Tachyzoite, ME49 merozoite, ME49 Oocyst, ME49 Bradyzoite. Gregory Hehl AB Fritz HM Sibley/Greg
Show/Hide expression data references
  • Hehl AB Asexual expansion of Toxoplasma gondii merozoites is distinct from tachyzoites and entails expression of non-overlapping gene families to attach, invade, and replicate within feline enterocytes.
  • Fritz HM Transcriptomic analysis of toxoplasma development reveals many novel functions and structures specific to sporozoites and oocysts.
  • Gregory ToxoDB
  • Sibley/Greg ToxoDB

Orthologs

Ortholog group members (OG5_128555)

Species Accession Gene Product
Arabidopsis thaliana AT5G38890   nucleic acid-binding, OB-fold-like protein
Arabidopsis thaliana AT5G18470   curculin-like (mannose-binding) lectin family protein
Babesia bovis BBOV_IV004430   conserved hypothetical protein
Brugia malayi Bm1_53645   3'-5' exoribonuclease CSL4 homolog
Candida albicans CaO19.1026   similar to S. cerevisiae CSL4 (YNL232W) exosome component involved mRNA degradation and nuclear RNA processing
Candida albicans CaO19.8628   similar to S. cerevisiae CSL4 (YNL232W) exosome component involved mRNA degradation and nuclear RNA processing
Caenorhabditis elegans CELE_Y48A6B.5   Protein EXOS-1
Dictyostelium discoideum DDB_G0285377   hypothetical protein
Drosophila melanogaster Dmel_CG6249   CG6249 gene product from transcript CG6249-RA
Echinococcus granulosus EgrG_000727700   exosome complex component CSL4
Echinococcus multilocularis EmuJ_000727700   exosome complex component CSL4
Homo sapiens 51013   exosome component 1
Loa Loa (eye worm) LOAG_02001   hypothetical protein
Mus musculus ENSMUSG00000034321   exosome component 1
Oryza sativa 4331133   Os02g0815800
Plasmodium berghei PBANKA_0617500   exosome complex component CSL4, putative
Plasmodium falciparum PF3D7_0720000   exosome complex component CSL4, putative
Plasmodium knowlesi PKNH_0315400   exosome complex component CSL4, putative
Plasmodium vivax PVX_096320   exosome complex component CSL4, putative
Plasmodium yoelii PY00332   3'-5' exoribonuclease csl4 homolog (ec 3.1.13.-) (cgi-108). [human, putative
Saccharomyces cerevisiae YNL232W   Csl4p
Schistosoma japonicum Sjp_0022800   ko:K01149 exosome component 1 [EC:3.1.13.-], putative
Schistosoma mansoni Smp_007540   3'-5' exonuclease
Toxoplasma gondii TGME49_203610   3'-5' exoribonuclease csl4, putative
Theileria parva TP01_0308   hypothetical protein
Trichomonas vaginalis TVAG_121320   conserved hypothetical protein
Trichomonas vaginalis TVAG_110240   conserved hypothetical protein

Essentiality

TGME49_203610 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
CELE_Y48A6B.5 Caenorhabditis elegans embryonic lethal wormbase
CELE_Y48A6B.5 Caenorhabditis elegans slow growth wormbase
YNL232W Saccharomyces cerevisiae inviable yeastgenome
PBANKA_0617500 Plasmodium berghei Essential plasmo
TGME49_203610 this record Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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
  • 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
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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.
  • 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
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan

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 TGME49_203610 (Toxoplasma gondii), 3'-5' exoribonuclease csl4, putative
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