Detailed view for PF3D7_1343900

Basic information

TDR Targets ID: 283
Plasmodium falciparum, U4/U6 small nuclear ribonucleoprotein PRP4, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 5.6872 | Length (AA): 648 | MW (Da): 76190 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | Predicted trans-membrane segments: 0

Druggability Group : DG3

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
PF08799   pre-mRNA processing factor 4 (PRP4) like

Gene Ontology

Mouse over links to read term descriptions.
GO:0005515   protein binding  
GO:0008380   RNA splicing  

Metabolic Pathways

Spliceosome (KEGG)

Structural information

Modbase 3D models:

There are 7 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
379 645 1vyh (C) 94 377 21.00 0 1 0.69 -0.27
425 647 2h14 (A) 34 252 29.00 0 1 0.73 -0.69
11 193 4tql (A) 43 238 15.00 0.016 0.03 0.372507 -0.32
54 216 4uos (A) 1 180 22.00 0.45 0.18 0.499643 -1.35
57 87 1mzw (B) 106 136 58.00 0.2 1 0.811239 -0.93
404 647 4lg8 (A) 232 471 23.00 0.000000047 1 0.672943 -0.16
4 193 4tql (A) 46 238 15.00 0.018 0.05 0.44111 -0.34

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 intra-erythrocytic - 0 hs, intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, Ring. Otto TD Zanghi G
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 24 hs, intra-erythrocytic - 32 hs, intra-erythrocytic - 48 hs, Male Gametocyte. Otto TD Lasonder E
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intra-erythrocytic - 40 hs, Oocyst, Sporozoite, Female Gametocyte. Otto TD Zanghi G Lasonder E
Show/Hide expression data references
  • Lasonder E Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes. Molecular insight into sex-specific processes and translational repression.
  • Otto TD New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.
  • Zanghi G A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection.

Orthologs

Ortholog group members (OG5_128652)

Species Accession Gene Product
Arabidopsis thaliana AT2G41500   splicing factor PRP4-like protein LACHESIS
Babesia bovis BBOV_I003610   WD domain, G-beta repeat domain containing protein
Brugia malayi Bm1_41875   U4/U6 small nuclear ribonucleoprotein hPrp4
Candida albicans CaO19.7343   WD40 repeat protein similar to S. cerevisiae PRP4 (YPR178W) spliceosomal U4/U6 snRNP 60 kd protein
Caenorhabditis elegans CELE_C36B1.5   Protein PRP-4
Cryptosporidium hominis Chro.50272   WD-40 repeat protein family / small nuclear ribonucleoprotein Prp4p-related
Cryptosporidium parvum cgd5_1130   WD-40 repeat protein family / small nuclear ribonucleoprotein Prp4p-related
Dictyostelium discoideum DDB_G0287635   U4/U6 small nuclear ribonucleoprotein
Drosophila melanogaster Dmel_CG6322   U4-U6 small nuclear riboprotein factor 60K
Echinococcus granulosus EgrG_000792350   U4:U6 small nuclear ribonucleoprotein Prp4
Entamoeba histolytica EHI_040300   WD domain containing protein
Echinococcus multilocularis EmuJ_000792350   U4:U6 small nuclear ribonucleoprotein Prp4
Homo sapiens ENSG00000136875   pre-mRNA processing factor 4
Loa Loa (eye worm) LOAG_05583   U4/U6 small nuclear ribonucleoprotein hPrp4
Mus musculus ENSMUSG00000066148   PRP4 pre-mRNA processing factor 4 homolog (yeast)
Neospora caninum NCLIV_018260   U4/U6 small nuclear ribonucleoprotein, putative
Oryza sativa 4332861   Os03g0355200
Plasmodium berghei PBANKA_1356900   U4/U6 small nuclear ribonucleoprotein PRP4, putative
Plasmodium falciparum PF3D7_1343900   U4/U6 small nuclear ribonucleoprotein PRP4, putative
Plasmodium knowlesi PKNH_1257500   U4/U6 small nuclear ribonucleoprotein PRP4, putative
Plasmodium vivax PVX_083090   U4/U6 small nuclear ribonucleoprotein PRP4, putative
Plasmodium yoelii PY05621   Homo sapiens RIKEN cDNA 1600015H11 gene-related
Saccharomyces cerevisiae YPR178W   Prp4p
Schistosoma japonicum Sjp_0310570   similar to UPF0458 protein C7orf42 homolog, putative
Schistosoma japonicum Sjp_0028890   ko:K08827 pre-mRNA-processing factor 4, putative
Schistosoma japonicum Sjp_0206580   Conserved hypothetical protein
Schistosoma mansoni Smp_169060   hypothetical protein
Schmidtea mediterranea mk4.000224.00   U4/U6 small nuclear ribonucleoprotein Prp4
Schmidtea mediterranea mk4.000224.02   U4/U6 small nuclear ribonucleoprotein Prp4
Toxoplasma gondii TGME49_243540   WD domain, G-beta repeat-containing protein
Theileria parva TP01_0483   hypothetical protein, conserved
Trichomonas vaginalis TVAG_063230   WD-repeat protein, putative

Essentiality

PF3D7_1343900 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
CELE_C36B1.5 Caenorhabditis elegans embryonic lethal wormbase
CELE_C36B1.5 Caenorhabditis elegans larval arrest wormbase
CELE_C36B1.5 Caenorhabditis elegans slow growth wormbase
CELE_C36B1.5 Caenorhabditis elegans sterile wormbase
YPR178W Saccharomyces cerevisiae inviable yeastgenome
PBANKA_1356900 Plasmodium berghei Essential plasmo
TGME49_243540 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
  • 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
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan

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 pre-mRNA processing factor 4 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

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Gene identifier PF3D7_1343900 (Plasmodium falciparum), U4/U6 small nuclear ribonucleoprotein PRP4, putative
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