Detailed view for Tb927.9.11110

Basic information

TDR Targets ID: 19693
Trypanosoma brucei, U5 snRNA-associated splicing factor
Source Database / ID:  TriTrypDB  GeneDB

pI: 8.4114 | Length (AA): 2403 | MW (Da): 276999 | Paralog Number: 0

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

PF08082   PRO8NT (NUC069), PrP8 N-terminal domain
PF08083   PROCN (NUC071) domain
PF08084   PROCT (NUC072) domain
PF10596   U6-snRNA interacting domain of PrP8
PF10597   U5-snRNA binding site 2 of PrP8
PF10598   RNA recognition motif of the spliceosomal PrP8
PF12134   PRP8 domain IV core

Gene Ontology

Mouse over links to read term descriptions.
GO:0030623   U5 snRNA binding  
GO:0017070   U6 snRNA binding  
GO:0000398   nuclear mRNA splicing, via spliceosome  
GO:0005681   spliceosome  
GO:0005515   protein binding  
GO:0003723   RNA binding  

Metabolic Pathways

Spliceosome (KEGG)

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
719 830 5j0l (C) 10 124 19.00 0.59 0.03 0.187708 -0.78
864 2384 4i43 (B) 885 2396 40.00 0 1 1.04506 -0.03
1821 2079 3e9l (A) 1760 2016 42.00 0 1 0.723882 -1.07
1902 2053 3lru (B) 1840 1990 43.00 0 1 0.327754 0.19

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 Procyclic. Siegel TN
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile 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_127578)

Species Accession Gene Product
Arabidopsis thaliana AT4G38780   Pre-mRNA-processing-splicing factor
Arabidopsis thaliana AT1G80070   putative splicing factor Prp8
Babesia bovis BBOV_IV007790   processing splicing factor 8, putative
Brugia malayi Bm1_41550   Pre-mRNA splicing factor PRP8
Candida albicans CaO19.13800   similar to S. cerevisiae PRP8 (YHR165C) crucial component of the spliceosome and U5 snRNP
Candida albicans CaO19.6442   similar to S. cerevisiae PRP8 (YHR165C) crucial component of the spliceosome and U5 snRNP
Caenorhabditis elegans CELE_C50C3.6   Protein PRP-8
Cryptosporidium hominis Chro.30328   ENSANGP00000005722
Cryptosporidium parvum cgd3_2890   Prp8. JAB/PAD domain
Dictyostelium discoideum DDB_G0274229   Mov34/MPN/PAD-1 domain-containing protein
Drosophila melanogaster Dmel_CG8877   pre-mRNA processing factor 8
Echinococcus granulosus EgrG_000151700   pre mRNA processing splicing factor 8
Entamoeba histolytica EHI_060350   splicing factor Prp8, putative
Echinococcus multilocularis EmuJ_000151700   pre mRNA processing splicing factor 8
Giardia lamblia GL50803_112114   Splicing factor-like protein, putative
Homo sapiens ENSG00000174231   pre-mRNA processing factor 8
Leishmania braziliensis LbrM.34.3940   PRP8 protein homologue, putative,U5 snRNA-associated splicing factor
Leishmania donovani LdBPK_354000.1   PRP8 protein homologue, putative
Leishmania infantum LinJ.35.4000   PRP8 protein homologue, putative,U5 snRNA-associated splicing factor
Leishmania major LmjF.35.3950   PRP8 protein homologue, putative,U5 snRNA-associated splicing factor
Leishmania mexicana LmxM.34.3950   PRP8 protein homologue, putative,U5 snRNA-associated splicing factor
Loa Loa (eye worm) LOAG_00327   pre-mRNA splicing factor PRP8
Mus musculus ENSMUSG00000020850   pre-mRNA processing factor 8
Neospora caninum NCLIV_031970   hypothetical protein
Oryza sativa 4340248   Os06g0167000
Oryza sativa 4337900   Os05g0163200
Plasmodium berghei PBANKA_1003100   pre-mRNA-processing-splicing factor 8, putative
Plasmodium falciparum PF3D7_0405400   pre-mRNA-processing-splicing factor 8, putative
Plasmodium knowlesi PKNH_0303500   pre-mRNA-processing-splicing factor 8, putative
Plasmodium vivax PVX_000970   pre-mRNA-processing-splicing factor 8, putative
Plasmodium yoelii PY01669   hypothetical protein
Saccharomyces cerevisiae YHR165C   U4/U6-U5 snRNP complex component PRP8
Schistosoma japonicum Sjp_0036700   Pre-mRNA-processing-splicing factor 8, putative
Schistosoma japonicum Sjp_0036690   Pre-mRNA-processing-splicing factor 8, putative
Schistosoma mansoni Smp_140890   splicing factor Prp8
Schmidtea mediterranea mk4.004704.01   Putative pre-mRNA splicing factor prp8
Schmidtea mediterranea mk4.002311.02   Pre-mRNA-splicing factor 8 homolog
Schmidtea mediterranea mk4.002311.03   Putative pre-mRNA splicing factor prp8
Schmidtea mediterranea mk4.003896.00  
Schmidtea mediterranea mk4.002311.01  
Schmidtea mediterranea mk4.006236.00  
Schmidtea mediterranea mk4.003280.00  
Schmidtea mediterranea mk4.012505.00   Putative pre-mRNA splicing factor prp8
Trypanosoma brucei gambiense Tbg972.9.6600   PRP8 protein homologue,U5 snRNA-associated splicing factor
Trypanosoma brucei Tb927.9.11110   U5 snRNA-associated splicing factor
Trypanosoma cruzi TcCLB.508461.320   U5 snRNA-associated splicing factor, putative
Toxoplasma gondii TGME49_231970   pre-mRNA processing splicing factor PRP8
Theileria parva TP03_0292   splicing factor Prp8, putative
Trichomonas vaginalis TVAG_206870   pre-mRNA splicing factor prp8, putative

Essentiality

Tb927.9.11110 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb09.211.2420 this record Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb09.211.2420 this record Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb09.211.2420 this record Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb09.211.2420 this record Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_C50C3.6 Caenorhabditis elegans embryonic lethal wormbase
CELE_C50C3.6 Caenorhabditis elegans larval arrest wormbase
CELE_C50C3.6 Caenorhabditis elegans slow growth wormbase
CELE_C50C3.6 Caenorhabditis elegans sterile wormbase
YHR165C Saccharomyces cerevisiae inviable yeastgenome
PBANKA_1003100 Plasmodium berghei Essential plasmo
TGME49_231970 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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
  • 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
  • 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
  • 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
  • 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

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 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

1 literature reference was collected for this gene.

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Gene identifier Tb927.9.11110 (Trypanosoma brucei), U5 snRNA-associated splicing factor
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