Detailed view for TcCLB.506649.80

Basic information

TDR Targets ID: 53646
Trypanosoma cruzi, Double RNA binding domain protein 3
Source Database / ID:  TriTrypDB  GeneDB

pI: 9.5384 | Length (AA): 325 | MW (Da): 36369 | Paralog Number: 1

Signal peptide: N | GPI Anchor: N | 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:0003676   nucleic acid binding  
GO:0000166   nucleotide binding  

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
34 147 1u6f (A) 1 116 20.00 0.0000001 0.93 0.53 0.02
75 156 1wex (A) 14 94 31.00 0.0000048 1 0.86 -2.26
76 255 1b7f (A) 124 289 16.00 0 1 0.7 -0.68
4 325 5lp2 (B) 64 424 10.00 0 0 1.01217 0.38
62 178 2n3o (A) 44 159 26.00 0 1 0.8178 -1.25
76 154 1h2v (Z) 39 120 22.00 0 1 0.594477 -1.7
76 313 3sde (B) 73 273 14.00 0 1 0.738708 0.35
275 312 5ctd (A) 3 45 47.00 0.26 0.12 0.380223 -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 80-100% percentile epimastigote, metacyclic. Smircich P
Show/Hide expression data references
  • Smircich P Ribosome profiling reveals translation control as a key mechanism generating differential gene expression in Trypanosoma cruzi.

Orthologs

Ortholog group members (OG5_127719)

Species Accession Gene Product
Arabidopsis thaliana AT1G43190   polypyrimidine tract-binding protein 3
Brugia malayi Bm1_11305   hypothetical protein
Caenorhabditis elegans CELE_D2089.4   Protein PTB-1, isoform A
Dictyostelium discoideum DDB_G0284321   RNA recognition motif-containing protein RRM
Drosophila melanogaster Dmel_CG31000   hephaestus
Echinococcus granulosus EgrG_000614400   Regulator of differentiation 1
Echinococcus multilocularis EmuJ_000614400   Regulator of differentiation 1
Homo sapiens ENSG00000117569   polypyrimidine tract binding protein 2
Homo sapiens ENSG00000119314   polypyrimidine tract binding protein 3
Homo sapiens ENSG00000011304   polypyrimidine tract binding protein 1
Leishmania braziliensis LbrM.04.1190   RNA-binding protein, putative
Leishmania braziliensis LbrM.32.0940   hypothetical protein, conserved
Leishmania donovani LdBPK_041190.1   Double RNA binding domain protein 3
Leishmania donovani LdBPK_320900.1   polypyrimidine tract-binding protein, putative
Leishmania infantum LinJ.04.1190   RNA-binding protein, putative
Leishmania infantum LinJ.32.0900   hypothetical protein, conserved
Leishmania major LmjF.04.1170   RNA-binding protein, putative
Leishmania major LmjF.32.0850   hypothetical protein, conserved
Leishmania mexicana LmxM.04.1170   RNA-binding protein, putative
Leishmania mexicana LmxM.31.0850   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_11032   hypothetical protein
Loa Loa (eye worm) LOAG_13430   hypothetical protein
Loa Loa (eye worm) LOAG_14331   hypothetical protein
Loa Loa (eye worm) LOAG_14332   hypothetical protein
Loa Loa (eye worm) LOAG_15376   hypothetical protein
Mus musculus ENSMUSG00000028382   polypyrimidine tract binding protein 3
Mus musculus ENSMUSG00000028134   polypyrimidine tract binding protein 2
Mus musculus ENSMUSG00000006498   polypyrimidine tract binding protein 1
Neospora caninum NCLIV_042650   GG11844, related
Oryza sativa 4338905   Os05g0437300
Oryza sativa 4325048   Os01g0867800
Onchocerca volvulus OVOC9716  
Plasmodium berghei PBANKA_0105200   polypyrimidine tract-binding protein, putative
Plasmodium falciparum PF3D7_0606500   polypyrimidine tract-binding protein, putative
Plasmodium knowlesi PKNH_1143700   polypyrimidine tract-binding protein, putative
Plasmodium vivax PVX_113495   polypyrimidine tract binding protein, putative
Plasmodium yoelii PY01048   neural polypyrimidine tract binding protein
Schistosoma japonicum Sjp_0120680   expressed protein
Schistosoma japonicum Sjp_0208600   Regulator of differentiation 1, putative
Schistosoma japonicum Sjp_0099930   Polypyrimidine tract-binding protein 1, putative
Schistosoma mansoni Smp_036590.2   polypyrimidine tract binding protein
Schistosoma mansoni Smp_138050.2   polypyrimidine tract binding protein
Schistosoma mansoni Smp_138050.1   polypyrimidine tract binding protein
Schmidtea mediterranea mk4.033658.00  
Schmidtea mediterranea mk4.017830.01  
Schmidtea mediterranea mk4.002486.04  
Schmidtea mediterranea mk4.025262.00   FI03683p
Schmidtea mediterranea mk4.001622.05  
Schmidtea mediterranea mk4.035163.00  
Schmidtea mediterranea mk4.001622.06  
Schmidtea mediterranea mk4.002647.00  
Schmidtea mediterranea mk4.013283.01  
Schmidtea mediterranea mk4.012260.00  
Schmidtea mediterranea mk4.001628.07  
Schmidtea mediterranea mk4.007390.00  
Trypanosoma brucei gambiense Tbg972.9.4840   RNA-binding protein, putative,DRBD4
Trypanosoma brucei gambiense Tbg972.11.15740   RNA-binding protein, putative,DRBD4
Trypanosoma brucei Tb927.9.8740   Double RNA binding domain protein 3
Trypanosoma brucei Tb927.11.14100   Double RNA-binding domain containing protein 4
Trypanosoma congolense TcIL3000.11.14390   polypyrimidine tract-binding protein, putative
Trypanosoma congolense TcIL3000_9_3060   Double RNA binding domain protein 3
Trypanosoma cruzi TcCLB.506649.80   Double RNA binding domain protein 3
Trypanosoma cruzi TcCLB.511727.160   polypyrimidine tract-binding protein, putative
Toxoplasma gondii TGME49_290660   RNA recognition motif-containing protein

Essentiality

TcCLB.506649.80 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb09.211.0560 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb09.211.0560 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb09.211.0560 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb09.211.0560 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
Tb11.01.5690 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb11.01.5690 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb11.01.5690 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb11.01.5690 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
PBANKA_0105200 Plasmodium berghei Dispensable plasmo
TGME49_290660 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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
  • 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
  • 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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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.

Phenotypes and Validation (curated)

We have no manually annotated phenotypes for this target. What does this mean? / Care to help?

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
Species Known druggable target Linked compounds Reference
Homo sapiens polypyrimidine tract binding protein 1 Compounds References
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

No literature references available for this target.

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

User comments

No user comments are available for this gene. Log in to add comments, or register.

Enter your comment

User ()
Gene identifier TcCLB.506649.80 (Trypanosoma cruzi), Double RNA binding domain protein 3
Title for this comment
Comment