Detailed view for Tb927.2.3880

Basic information

TDR Targets ID: 55130
Trypanosoma brucei, heterogeneous nuclear ribonucleoproteins F/H homologue
Source Database / ID:  TriTrypDB  GeneDB

pI: 6.7357 | Length (AA): 487 | MW (Da): 55135 | 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

PF00076   RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)

Gene Ontology

Mouse over links to read term descriptions.
GO:0003729   mRNA binding  
GO:0005634   nucleus  
GO:0003676   nucleic acid binding  
GO:0000166   nucleotide binding  
GO:0006396   RNA processing  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in KEGG.

Structural information

Modbase 3D models:

There are 8 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
2 108 1n54 (B) 11 125 21.00 0 1 0.433862 -0.36
5 191 3smz (A) 41 205 28.00 0.0018 1 0.496497 0.57
6 112 2l9w (A) 294 398 14.00 0 0.47 0.389862 -0.59
17 85 2cph (A) 454 524 30.00 0.12 0.66 0.450693 0.27
24 191 2qfj (A) 109 282 24.00 0.015 1 0.559562 0.25
31 90 2dgs (A) 119 178 28.00 0.38 0.65 0.360251 0.68
383 470 2lxu (A) 7 96 39.00 0 1 0.708928 -1.18
387 469 5uzm (A) 146 230 51.00 0 1 0.838382 -0.88

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 Bloodstream Form. Siegel TN
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile Procyclic. 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_129021)

Species Accession Gene Product
Arabidopsis thaliana AT5G66010   RNA recognition motif-containing protein
Brugia malayi Bm1_32715   RNA recognition motif.
Brugia malayi Bm1_12005   RNA binding protein
Brugia malayi Bm1_48255   Heterogeneous nuclear ribonucleoprotein H'
Caenorhabditis elegans CELE_Y73B6BL.33   Protein HRPF-2
Drosophila melanogaster Dmel_CG6946   glorund
Echinococcus granulosus EgrG_000083900   heterogeneous nuclear ribonucleoprotein
Echinococcus multilocularis EmuJ_000083900   heterogeneous nuclear ribonucleoprotein
Homo sapiens ENSG00000126945   heterogeneous nuclear ribonucleoprotein H2 (H')
Homo sapiens ENSG00000169813   heterogeneous nuclear ribonucleoprotein F
Homo sapiens ENSG00000169045   heterogeneous nuclear ribonucleoprotein H1 (H)
Loa Loa (eye worm) LOAG_07344   RNA binding protein
Loa Loa (eye worm) LOAG_12543   hypothetical protein
Loa Loa (eye worm) LOAG_11458   hypothetical protein
Loa Loa (eye worm) LOAG_11457   hypothetical protein
Loa Loa (eye worm) LOAG_00436   heterogeneous nuclear ribonucleoprotein H
Mus musculus ENSMUSG00000007850   heterogeneous nuclear ribonucleoprotein H1
Mus musculus ENSMUSG00000042079   heterogeneous nuclear ribonucleoprotein F
Mus musculus ENSMUSG00000045427   heterogeneous nuclear ribonucleoprotein H2
Neospora caninum NCLIV_050590   GL11864, related
Neospora caninum NCLIV_001680   RRM domain-containing protein, putative
Onchocerca volvulus OVOC9534  
Onchocerca volvulus OVOC3029  
Plasmodium berghei PBANKA_0508400   RNA-binding protein, putative
Plasmodium falciparum PF3D7_1024200   RNA-binding protein, putative
Plasmodium knowlesi PKNH_0608700   RNA-binding protein, putative
Plasmodium vivax PVX_111500   RNA-binding protein, putative
Schistosoma japonicum Sjp_0023270   Heterogeneous nuclear ribonucleoprotein F, putative
Schistosoma mansoni Smp_179270.1   heterogeneous nuclear ribonucleoprotein
Schistosoma mansoni Smp_179270.2   heterogeneous nuclear ribonucleoprotein
Schistosoma mansoni Smp_179270.3   heterogeneous nuclear ribonucleoprotein
Schmidtea mediterranea mk4.011751.02   G-rich sequence factor 1
Schmidtea mediterranea mk4.000502.07  
Trypanosoma brucei gambiense Tbg.972.2.2100   heterogeneous nuclear ribonucleoprotein H/F, putative
Trypanosoma brucei Tb927.2.3880   heterogeneous nuclear ribonucleoproteins F/H homologue
Trypanosoma congolense TcIL3000_0_16520   heterogeneous nuclear ribonucleoprotein H/F, putative
Trypanosoma cruzi TcCLB.504157.10   heterogeneous nuclear ribonucleoprotein H/F, putative
Trypanosoma cruzi TcCLB.511109.130   heterogeneous nuclear ribonucleoprotein H/F, putative
Toxoplasma gondii TGME49_236540   RNA recognition motif-containing protein
Toxoplasma gondii TGME49_294812   RNA recognition motif-containing protein

Essentiality

Tb927.2.3880 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb927.2.3880 this record Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.2.3880 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.2.3880 this record Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.2.3880 this record Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_Y73B6BL.33 Caenorhabditis elegans embryonic lethal wormbase
PBANKA_0508400 Plasmodium berghei Essential plasmo
TGME49_294812 Toxoplasma gondii Probably essential sidik
TGME49_236540 Toxoplasma gondii Probably essential sidik
TGME49_294812 Toxoplasma gondii Probably non-essential sidik
TGME49_236540 Toxoplasma gondii Probably non-essential sidik
TGME49_294812 Toxoplasma gondii Essentiality uncertain sidik
TGME49_236540 Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan

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 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) 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.

If you have references for this gene, please enter them in a user comment (below) or Contact us.

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Gene identifier Tb927.2.3880 (Trypanosoma brucei), heterogeneous nuclear ribonucleoproteins F/H homologue
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