Detailed view for Tb927.3.1930

Basic information

TDR Targets ID: 11035
Trypanosoma brucei, pre-mrna-processing factor 17
Source Database / ID:  TriTrypDB  GeneDB

pI: 8.2774 | Length (AA): 479 | MW (Da): 52823 | 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

PF00400   WD domain, G-beta repeat

Gene Ontology

Mouse over links to read term descriptions.
GO:0071013   GO:catalytic step 2 spliceosome  

GO:0008150   biological_process  
GO:0005575   cellular_component  
GO:0003674   molecular_function  
GO:0000398   nuclear mRNA splicing, via spliceosome  
GO:0005515   protein binding  

Metabolic Pathways

Spliceosome (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
208 518 5kdo (B) 44 339 21.00 0.000000075 1 0.866629 -0.34
264 300 5cxb (B) 449 485 38.00 0.63 0.28 0.553691 -0.81
267 298 4bh6 (A) 514 545 34.00 0 0.25 0.523457 -1.1

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_128322)

Species Accession Gene Product
Arabidopsis thaliana AT1G10580   transducin/WD40 repeat-like superfamily protein
Babesia bovis BBOV_III005380   WD domain, G-beta repeat containing protein
Brugia malayi Bm1_54120   pre-mRNA splicing factor
Candida albicans CaO19.13703   member of the beta transducin family involved in pre-mRNA splicing
Candida albicans CaO19.6347   member of the beta transducin family involved in pre-mRNA splicing
Caenorhabditis elegans CELE_F49D11.1   Protein PRP-17
Cryptosporidium hominis Chro.10205   transducin / WD-40 repeat protein family
Cryptosporidium parvum cgd1_1800   transducin / WD-40 repeat protein family
Dictyostelium discoideum DDB_G0289501   WD40 repeat-containing protein
Drosophila melanogaster Dmel_CG6015   CG6015 gene product from transcript CG6015-RA
Echinococcus granulosus EgrG_000188400   pre mRNA processing factor 17
Entamoeba histolytica EHI_126260   WD domain containing protein
Echinococcus multilocularis EmuJ_000188400   pre mRNA processing factor 17
Homo sapiens ENSG00000168438   cell division cycle 40
Leishmania braziliensis LbrM.25.1410   hypothetical protein, conserved
Leishmania donovani LdBPK_251930.1   hypothetical protein, conserved
Leishmania infantum LinJ.25.1930   hypothetical protein, conserved
Leishmania major LmjF.25.1850   hypothetical protein, conserved
Leishmania mexicana LmxM.25.1850   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_12200   pre-mRNA splicing factor
Loa Loa (eye worm) LOAG_11526   hypothetical protein
Mus musculus ENSMUSG00000038446   cell division cycle 40
Neospora caninum NCLIV_039860   pre-mRNA splicing factor, putative
Oryza sativa 4333045   Os03g0397500
Onchocerca volvulus OVOC161  
Plasmodium berghei PBANKA_1435300   pre-mRNA-processing factor 17, putative
Plasmodium falciparum PF3D7_1220100   pre-mRNA-processing factor 17, putative
Plasmodium knowlesi PKNH_1439300   pre-mRNA-processing factor 17, putative
Plasmodium vivax PVX_123645   pre-mRNA splicing factor PRP17, putative
Plasmodium yoelii PY01805   Arabidopsis thaliana T10O24.21-related
Saccharomyces cerevisiae YDR364C   Cdc40p
Schistosoma japonicum Sjp_0301150   Pre-mRNA-processing factor 17, putative
Schistosoma mansoni Smp_074370   hypothetical protein
Schmidtea mediterranea mk4.002976.03  
Schmidtea mediterranea mk4.007569.00  
Trypanosoma brucei gambiense Tbg972.3.1850   hypothetical protein, conserved
Trypanosoma brucei Tb927.3.1930   pre-mrna-processing factor 17
Trypanosoma congolense TcIL3000_3_1030   hypothetical protein, conserved
Trypanosoma cruzi TcCLB.504045.10   hypothetical protein, conserved
Toxoplasma gondii TGME49_265410   G-protein beta WD-40 repeat containing protein
Theileria parva TP02_0409   hypothetical protein
Trichomonas vaginalis TVAG_447010   pre-mRNA splicing factor prp17, putative

Essentiality

Tb927.3.1930 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb927.3.1930 this record Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.3.1930 this record Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.3.1930 this record Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.3.1930 this record Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_F49D11.1 Caenorhabditis elegans embryonic lethal wormbase
CELE_F49D11.1 Caenorhabditis elegans larval arrest wormbase
CELE_F49D11.1 Caenorhabditis elegans sterile wormbase
YDR364C Saccharomyces cerevisiae inviable yeastgenome
PBANKA_1435300 Plasmodium berghei Essential plasmo
TGME49_265410 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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.
  • 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
  • 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.

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) 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 procyclic forms . 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 Tb927.3.1930 (Trypanosoma brucei), pre-mrna-processing factor 17
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