Detailed view for Tb11.v5.0171

Basic information

TDR Targets ID: 17392
Trypanosoma brucei, 5'-3' exonuclease XRNA, putative

Source Database / ID:  TriTrypDB  GeneDB

pI: 7.7982 | Length (AA): 1418 | MW (Da): 158671 | Paralog Number: 1

Signal peptide: N | GPI Anchor: | 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

PF03159   XRN 5'-3' exonuclease N-terminus

Gene Ontology

Mouse over links to read term descriptions.
GO:0005622   intracellular  
GO:0003676   nucleic acid binding  
GO:0004527   exonuclease activity  

Metabolic Pathways

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
1 1203 2y35 (A) 1 1138 35.00 0 1 0.998578 0.51
4 643 5fir (A) 4 761 38.00 0 1 0.79934 -0.37
1248 1374 3a21 (A) 388 521 31.00 0.16 0.37 0.279363 0.21

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
Lower 20-40% percentile Procyclic, Bloodstream Form. Siegel TN
Show/Hide expression data references
  • Siegel TN Genome-wide analysis of mRNA abundance in two life-cycle stages of Trypanosoma brucei and identification of splicing and polyadenylation sites.

Orthologs

Ortholog group members (OG5_126774)

Species Accession Gene Product
Arabidopsis thaliana AT1G75660   5'-3' exoribonuclease 3
Arabidopsis thaliana AT5G42540   5'-3' exoribonuclease 2
Arabidopsis thaliana AT1G54490   5'-3' exoribonuclease 4
Babesia bovis BBOV_II002230   XRN 5'-3' exonuclease protein, putative
Babesia bovis BBOV_II007140   5'-3' exoribonuclease (XRN2), putative
Brugia malayi Bm1_49855   5'-3' exoribonuclease 2
Candida albicans CaO19.12434   likely 5'-3' exoribonuclease, similar to S. cerevisiae KEM1 (YGL173C)
Candida albicans CaO19.4681   likely 5'-3' exoribonuclease, similar to S. cerevisiae RAT1 (YOR048C)
Candida albicans CaO19.4969   likely 5'-3' exoribonuclease, similar to S. cerevisiae KEM1 (YGL173C)
Candida albicans CaO19.12150   likely 5'-3' exoribonuclease, similar to S. cerevisiae RAT1 (YOR048C)
Caenorhabditis elegans CELE_Y48B6A.3   Protein XRN-2
Caenorhabditis elegans CELE_Y39G8C.1   Protein XRN-1
Cryptosporidium hominis Chro.60243   hypothetical protein
Cryptosporidium hominis Chro.80264   CG10354-PA
Cryptosporidium hominis Chro.80265   pacman protein
Cryptosporidium parvum cgd8_2250   Rat1 Kar1/Rat1 like 5-3 exonuclease
Cryptosporidium parvum cgd6_2080   Kem1p-like 5-3 exonuclease
Dictyostelium discoideum DDB_G0276137   5'-3' exoribonuclease
Dictyostelium discoideum DDB_G0269922   5'-3' exoribonuclease
Drosophila melanogaster Dmel_CG10354   CG10354 gene product from transcript CG10354-RA
Drosophila melanogaster Dmel_CG3291   pacman
Echinococcus granulosus EgrG_000065500   5' 3' exoribonuclease 2
Echinococcus granulosus EgrG_000228400   5' 3' exoribonuclease 1
Entamoeba histolytica EHI_132400   5-3 exonuclease domain containing protein
Entamoeba histolytica EHI_133330   5-3 exonuclease domain containing protein
Entamoeba histolytica EHI_128220   5-3 exonuclease domain containing protein
Echinococcus multilocularis EmuJ_000065500   5' 3' exoribonuclease 2
Echinococcus multilocularis EmuJ_000228400   5' 3' exoribonuclease 1
Giardia lamblia GL50803_24133   5-3 exoribonuclease 2
Homo sapiens ENSG00000088930   5'-3' exoribonuclease 2
Homo sapiens ENSG00000114127   5'-3' exoribonuclease 1
Leishmania braziliensis LbrM.35.1980   exoribonuclease 2, putative
Leishmania braziliensis LbrM.06.0240   5-3 exonuclease, putative
Leishmania donovani LdBPK_060260.1   5'-3' exoribonuclease A, putative
Leishmania donovani LdBPK_361870.1   5'-3' exoribonuclease D, putative
Leishmania infantum LinJ.36.1870   exoribonuclease 2, putative
Leishmania infantum LinJ.06.0260   5-3 exonuclease, putative
Leishmania major LmjF.36.1790   exoribonuclease 2, putative
Leishmania major LmjF.06.0260   5-3 exonuclease, putative
Leishmania mexicana LmxM.36.1790   exoribonuclease 2, putative
Leishmania mexicana LmxM.06.0260   5-3 exonuclease, putative
Loa Loa (eye worm) LOAG_09226   hypothetical protein
Loa Loa (eye worm) LOAG_10183   hypothetical protein
Loa Loa (eye worm) LOAG_10732   hypothetical protein
Loa Loa (eye worm) LOAG_04889   single-stranded RNA 5'-3' exonuclease
Mus musculus ENSMUSG00000027433   5'-3' exoribonuclease 2
Mus musculus ENSMUSG00000032410   5'-3' exoribonuclease 1
Neospora caninum NCLIV_070100   GF20490, related
Neospora caninum NCLIV_017830   5-3 exonuclease, putative
Oryza sativa 4334408   Os03g0794800
Oryza sativa 4324952   Os01g0872700
Plasmodium berghei PBANKA_0940600   exonuclease, putative
Plasmodium berghei PBANKA_0810600   exoribonuclease, putative
Plasmodium falciparum PF3D7_0909400   exoribonuclease, putative
Plasmodium falciparum PF3D7_1106300   exonuclease, putative
Plasmodium knowlesi PKNH_0903900   exonuclease, putative
Plasmodium knowlesi PKNH_0707400   exoribonuclease, putative
Plasmodium vivax PVX_098910   exoribonuclease, putative
Plasmodium yoelii PY03131   Drosophila melanogaster CG10354 gene product-related
Saccharomyces cerevisiae YGL173C   Xrn1p
Saccharomyces cerevisiae YOR048C   Rat1p
Schistosoma japonicum Sjp_0075730   ko:K01146 5'-3' exoribonuclease 2 [EC:3.1.11.-], putative
Schistosoma mansoni Smp_133300   5'-3' exoribonuclease
Schmidtea mediterranea mk4.000444.11  
Schmidtea mediterranea mk4.000444.09   5'-3' exoribonuclease 1
Schmidtea mediterranea mk4.010275.01   5'-3' exoribonuclease 2
Schmidtea mediterranea mk4.009587.01   5'-3' exoribonuclease 2 homolog
Schmidtea mediterranea mk4.010275.00   5'-3' exoribonuclease 2
Trypanosoma brucei gambiense Tbg972.10.7600   5-3 exoribonuclease XRND, putative,5-3 exoribonuclease 2, putative
Trypanosoma brucei gambiense Tbg972.7.5630   5-3 exonuclease XRNA, putative,exoribonuclease 1, putative
Trypanosoma brucei Tb927.10.6220   5'-3' exoribonuclease D
Trypanosoma brucei Tb11.v5.0171   5'-3' exonuclease XRNA, putative
Trypanosoma congolense TcIL3000_10_5280   5'-3' exoribonuclease D, putative
Trypanosoma congolense TcIL3000_7_4080   5'-3' exoribonuclease A, putative
Trypanosoma cruzi TcCLB.507641.80   5'-3' exoribonuclease D, putative
Toxoplasma gondii TGME49_242830   XRN 5'-3' exonuclease N-terminus protein
Toxoplasma gondii TGME49_305780   5'-3' exoribonuclease, putative
Toxoplasma gondii TGME49_327600   hypothetical protein
Theileria parva TP02_0165   hypothetical protein
Theileria parva TP04_0369   exoribonuclease, putative
Trichomonas vaginalis TVAG_268140   5'->3' exoribonuclease, putative
Trichomonas vaginalis TVAG_124030   5'->3' exoribonuclease, putative
Trichomonas vaginalis TVAG_102480   5'->3' exoribonuclease, putative

Essentiality

Tb11.v5.0171 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb927.10.6220 Trypanosoma brucei significant gain of fitness in bloodstream forms (3 days) alsford
Tb927.10.6220 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb927.10.6220 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.10.6220 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
Tb927.7.4900 this record Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.7.4900 this record Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.7.4900 this record Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.7.4900 this record Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_Y48B6A.3 Caenorhabditis elegans embryonic lethal wormbase
CELE_Y48B6A.3 Caenorhabditis elegans larval arrest wormbase
CELE_Y48B6A.3 Caenorhabditis elegans larval lethal wormbase
CELE_Y48B6A.3 Caenorhabditis elegans slow growth wormbase
CELE_Y48B6A.3 Caenorhabditis elegans sterile wormbase
CELE_Y39G8C.1 Caenorhabditis elegans embryonic lethal wormbase
CELE_Y39G8C.1 Caenorhabditis elegans larval arrest wormbase
YOR048C Saccharomyces cerevisiae inviable yeastgenome
PBANKA_0810600 Plasmodium berghei Essential plasmo
TGME49_242830 Toxoplasma gondii Probably essential sidik
TGME49_305780 Toxoplasma gondii Probably essential sidik
TGME49_327600 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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)

Annotated phenotypes:

Affected Entity Phenotypic quality Occurs in Occurs at Evidence Observed in Drugs/Inhibitors
cell proliferation (GO:0008283) decreased (PATO:0000468) bloodstream stage trypomastigotes (PLO:0027) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: decreased cell proliferation (significant loss of fitness) in bloodstream forms (stage 6 days). References: 21363968
cell proliferation (GO:0008283) decreased (PATO:0000468) procyclic (PLO:0034) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: decreased cell proliferation (significant loss of fitness) in procyclic forms . References: 21363968
cell proliferation (GO:0008283) normal (PATO:0000461) procyclic (PLO:0034) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: normal cell proliferation (no significant loss or gain of fitness) in differentiation of procyclic to bloodstream forms . References: 21363968

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

5 literature references were collected for this gene.

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Gene identifier Tb11.v5.0171 (Trypanosoma brucei), 5'-3' exonuclease XRNA, putative
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