Detailed view for Tb927.9.9970

Basic information

TDR Targets ID: 11475
Trypanosoma brucei, Small nuclear RNA gene activation protein (SNAP) 50
Source Database / ID:  TriTrypDB  GeneDB

pI: 5.9644 | Length (AA): 448 | MW (Da): 51135 | 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

PF12251   snRNA-activating protein of 50kDa MW C terminal

Gene Ontology

Mouse over links to read term descriptions.
GO:0009301   snRNA transcription  
GO:0005634   nucleus  
GO:0003677   DNA binding  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in 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
16 158 5cwm (A) 90 227 14.00 0.15 0.09 0.502996 -0.86
42 140 4qan (A) 88 175 33.00 0.53 0.28 0.304082 0.97
78 168 5uh7 (A) 66 152 32.00 0.63 0.97 0.654225 -0.82
79 178 5szg (A) 1867 1976 19.00 0 0.06 0.495214 -1.01

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 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_129228)

Species Accession Gene Product
Arabidopsis thaliana AT1G28560   protein shoot redifferentiation defective 2
Babesia bovis BBOV_III010690   hypothetical protein
Brugia malayi Bm1_46635   hypothetical protein
Caenorhabditis elegans CELE_B0273.3   Protein B0273.3
Caenorhabditis elegans CELE_Y48G1BM.1   Protein Y48G1BM.1
Caenorhabditis elegans CELE_T02C12.2   Protein T02C12.2
Cryptosporidium hominis Chro.70130   hypothetical protein
Cryptosporidium parvum cgd7_1050   hypothetical protein
Dictyostelium discoideum DDB_G0274687   hypothetical protein
Drosophila melanogaster Dmel_CG42515   PSEA-binding protein 49kD
Drosophila melanogaster Dmel_CG42516   CG42516 gene product from transcript CG42516-RB
Echinococcus granulosus EgrG_000128600   expressed conserved protein
Echinococcus granulosus EgrG_000128500   snRNA activating protein complex subunit 3
Entamoeba histolytica EHI_197110   snRNA activating protein complex subunit, putative
Echinococcus multilocularis EmuJ_000128500   snRNA activating protein complex subunit 3
Echinococcus multilocularis EmuJ_000128600   expressed conserved protein
Homo sapiens 6619   small nuclear RNA activating complex, polypeptide 3, 50kDa
Leishmania braziliensis LbrM.34.4640   small nuclear RNA gene activation protein (SNAP) 50, putative
Leishmania donovani LdBPK_354730.1   small nuclear RNA gene activation protein (SNAP) 50, putative
Leishmania infantum LinJ.35.4730   small nuclear RNA gene activation protein (SNAP) 50, putative
Leishmania major LmjF.35.4660   small nuclear RNA gene activation protein (SNAP) 50, putative
Leishmania mexicana LmxM.34.4660   small nuclear RNA gene activation protein (SNAP) 50, putative
Loa Loa (eye worm) LOAG_10462   hypothetical protein
Mus musculus ENSMUSG00000028483   small nuclear RNA activating complex, polypeptide 3
Oryza sativa 4324317   Os01g0912600
Plasmodium berghei PBANKA_1324500   snRNA-activating protein complex subunit 3, putative
Plasmodium falciparum PF3D7_1460800   snRNA-activating protein complex subunit 3, putative
Plasmodium knowlesi PKNH_1220900   snRNA-activating protein complex subunit 3, putative
Plasmodium vivax PVX_117415   snRNA-activating protein complex subunit 3, putative
Plasmodium yoelii PY05165   hypothetical protein
Schistosoma japonicum Sjp_0214600   snRNA-activating protein complex subunit 3, putative
Schistosoma mansoni Smp_092780.1   hypothetical protein
Schistosoma mansoni Smp_092780.2   hypothetical protein
Schmidtea mediterranea mk4.010426.00   snRNA-activating protein complex subunit 3
Trypanosoma brucei gambiense Tbg972.9.5750   small nuclear RNA gene activation protein (SNAP) 50, putative
Trypanosoma brucei Tb927.9.9970   Small nuclear RNA gene activation protein (SNAP) 50
Trypanosoma congolense TcIL3000_9_3640   small nuclear RNA gene activation protein 50 (EMBL:AJ581666)
Trypanosoma cruzi TcCLB.510731.50   small nuclear RNA gene activation protein (SNAP) 50, putative
Trypanosoma cruzi TcCLB.506887.60   small nuclear RNA gene activation protein (SNAP) 50, putative
Theileria parva TP02_0077   hypothetical protein

Essentiality

Tb927.9.9970 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb09.211.1510 this record Trypanosoma brucei significant gain of fitness in bloodstream forms (3 days) alsford
Tb09.211.1510 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb09.211.1510 this record Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb09.211.1510 this record Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_T02C12.2 Caenorhabditis elegans embryonic lethal wormbase
CELE_T02C12.2 Caenorhabditis elegans larval arrest wormbase
CELE_T02C12.2 Caenorhabditis elegans larval lethal wormbase
CELE_T02C12.2 Caenorhabditis elegans slow growth wormbase
CELE_T02C12.2 Caenorhabditis elegans sterile wormbase
Show/Hide essentiality data references
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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.
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
  • 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
  • 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.
  • 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:

Affected Entity Phenotypic quality Occurs in Occurs at Evidence Observed in Drugs/Inhibitors
cell proliferation (GO:0008283) increased (PATO:0000470) 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: increased cell proliferation (significant gain of fitness) in bloodstream forms (stage 3 days). References: 21363968
cell proliferation (GO:0008283) normal (PATO:0000461) 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: normal cell proliferation (no significant loss or gain 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) increased (PATO:0000470) procyclic (PLO:0034) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: increased cell proliferation (significant 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

1 literature reference was collected for this gene.

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Gene identifier Tb927.9.9970 (Trypanosoma brucei), Small nuclear RNA gene activation protein (SNAP) 50
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