Detailed view for Tb927.11.11030
Basic information
Trypanosoma brucei, exosome-associated protein 4
Source Database / ID: TriTrypDB GeneDB
pI: 5.312 |
Length (AA): 232 |
MW (Da): 24758 |
Paralog Number:
0
Signal peptide: N | GPI Anchor: | Predicted trans-membrane segments: 0
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
Network
Pfam domains
Gene Ontology
GO:0000176 nuclear exosome (RNase complex)
GO:0003723 RNA binding
GO:0000175 3'-5'-exoribonuclease activity
GO:0006396 RNA processing
GO:0006364 rRNA processing
Metabolic Pathways
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 |
|---|---|---|---|---|---|---|---|---|---|
| 1 | 230 | 2br2 (B) | 12 | 240 | 26.00 | 0 | 1 | 1.36488 | -0.41 |
| 4 | 230 | 2po1 (A) | 13 | 238 | 25.00 | 0 | 1 | 1.35895 | -0.58 |
| 7 | 225 | 3b4t (A) | 2 | 234 | 19.00 | 0 | 0.99 | 1.11447 | 0.02 |
| 11 | 185 | 2nn6 (F) | 29 | 216 | 36.00 | 0 | 1 | 1.09151 | 0.65 |
Help me make sense of these data.
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:
Expression
| Upregulation Percent | Ranking | Stage | Dataset |
|---|---|---|---|
| Upper 80-100% percentile | Bloodstream Form. | Siegel TN |
| Upregulation Percent | Ranking | Stage | Dataset |
|---|---|---|---|
| Upper 60-80% percentile | Procyclic. | Siegel TN |
-
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_128529)
| Species | Accession | Gene Product |
|---|---|---|
| Arabidopsis thaliana | AT4G27490 | 3'-5'-exoribonuclease family protein |
| Babesia bovis | BBOV_III011810 | conserved hypothetical protein |
| Brugia malayi | Bm1_24220 | 3' exoribonuclease family, domain 1 containing protein |
| Candida albicans | CaO19.7801 | similar to S. cerevisiae MTR3 (YGR158C) exosome component involved mRNA degradation and nuclear RNA processing |
| Candida albicans | CaO19.168 | similar to S. cerevisiae MTR3 (YGR158C) exosome component involved mRNA degradation and nuclear RNA processing |
| Caenorhabditis elegans | CELE_Y6D11A.1 | Protein EXOS-4.2 |
| Cryptosporidium hominis | Chro.60409 | ribonuclease PH-like protein |
| Cryptosporidium parvum | cgd6_3540 | archeo-eukaryotice exosomal RNAse PH |
| Dictyostelium discoideum | DDB_G0271396 | hypothetical protein |
| Drosophila melanogaster | Dmel_CG8025 | CG8025 gene product from transcript CG8025-RA |
| Echinococcus granulosus | EgrG_000720150 | Exosome complex exonuclease MTR3 |
| Entamoeba histolytica | EHI_166910 | 3 exoribonuclease family protein |
| Entamoeba histolytica | EHI_126330 | 3 exoribonuclease family protein |
| Echinococcus multilocularis | EmuJ_000720150 | Exosome complex exonuclease MTR3 |
| Homo sapiens | 118460 | exosome component 6 |
| Leishmania braziliensis | LbrM.35.5140 | exosome-associated protein 4, putative |
| Leishmania donovani | LdBPK_365120.1 | exosome-associated protein 4, putative |
| Leishmania infantum | LinJ.36.5120 | exosome-associated protein 4, putative |
| Leishmania major | LmjF.36.4895 | exosome-associated protein 4, putative |
| Leishmania mexicana | LmxM.36.4895 | exosome-associated protein 4, putative |
| Loa Loa (eye worm) | LOAG_05308 | hypothetical protein |
| Mus musculus | 72544 | exosome component 6 |
| Neospora caninum | NCLIV_010510 | 3 exoribonuclease, putative |
| Oryza sativa | 9269241 | Os03g0844450 |
| Oryza sativa | 4344519 | Os08g0116800 |
| Plasmodium berghei | PBANKA_0306300 | 3' exoribonuclease, putative |
| Plasmodium falciparum | PF3D7_0209200 | 3'exoribonuclease, putative |
| Plasmodium knowlesi | PKNH_0411900 | 3'exoribonuclease, putative |
| Plasmodium yoelii | PY00320 | hypothetical protein |
| Saccharomyces cerevisiae | YGR158C | Mtr3p |
| Schistosoma japonicum | Sjp_0025350 | Exosome complex exonuclease MTR3, putative |
| Schistosoma japonicum | Sjp_0310060 | ko:K01149 exosome component 6 [EC:3.1.13.-], putative |
| Schistosoma mansoni | Smp_120960.2 | ribonuclease pH related |
| Schistosoma mansoni | Smp_120960.3 | ribonuclease pH related |
| Schistosoma mansoni | Smp_120960.1 | ribonuclease pH related |
| Schmidtea mediterranea | mk4.000842.05 | Exosome complex component MTR3 |
| Trypanosoma brucei gambiense | Tbg972.11.12360 | exosome-associated protein 4, putative |
| Trypanosoma brucei | Tb927.11.11030 | exosome-associated protein 4 |
| Trypanosoma congolense | TcIL3000.11.11750 | exosome-associated protein 4 |
| Trypanosoma cruzi | TcCLB.508269.60 | exosome-associated protein 4, putative |
| Trypanosoma cruzi | TcCLB.507841.34 | exosome-associated protein 4, putative |
| Toxoplasma gondii | TGME49_319650 | 3' exoribonuclease family, domain 1 domain-containing protein |
| Theileria parva | TP01_1052 | hypothetical protein |
| Trichomonas vaginalis | TVAG_441560 | conserved hypothetical protein |
Essentiality
| Gene/Ortholog | Organism | Phenotype | Source Study |
|---|---|---|---|
| Tb11.01.2820 this record | Trypanosoma brucei | no significant loss or gain of fitness in bloodstream forms (3 days) | alsford |
| Tb11.01.2820 this record | Trypanosoma brucei | significant loss of fitness in bloodstream forms (6 days) | alsford |
| Tb11.01.2820 this record | Trypanosoma brucei | significant loss of fitness in procyclic forms | alsford |
| Tb11.01.2820 this record | Trypanosoma brucei | no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms | alsford |
| YGR158C | Saccharomyces cerevisiae | inviable | yeastgenome |
| PBANKA_0306300 | Plasmodium berghei | Essential | plasmo |
| TGME49_319650 | Toxoplasma gondii | Probably essential | sidik |
-
wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170 -
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 -
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 -
nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource -
neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs -
keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection -
alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
Phenotypes and Validation (curated)
Annotated phenotypes:
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
Associated compounds / Druggability
Known modulators for this target
Predicted associations
By orthology with druggable targets
By sequence similarity to non orthologous druggable targets
Obtained from network model
Assayability
Assay information
Reagent availability
Bibliographic References
1 literature reference was collected for this gene.