Detailed view for PF3D7_1454000

Basic information

TDR Targets ID: 2843
Plasmodium falciparum, RNA-binding protein, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 5.2533 | Length (AA): 511 | MW (Da): 59423 | Paralog Number: 0

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)
PF01585   G-patch domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0008150   biological_process  
GO:0005622   intracellular  
GO:0003723   RNA binding  
GO:0003676   nucleic acid binding  
GO:0000166   nucleotide binding  

Metabolic Pathways

Spliceosome (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
414 509 1opi (A) 373 474 29.00 0 1 0.59 -0.85
124 304 4uos (A) 2 184 17.00 0.061 0.14 0.646907 -1.74
411 511 2pe8 (A) 299 399 32.00 0.00000000027 1 0.667352 -1.25
437 497 4a8x (A) 176 236 26.00 0.64 0.85 0.396874 0.38

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, merozoite, early ring, late ring, Ring, Female Gametocyte, Male Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 24 hs, intra-erythrocytic - 32 hs, sporozoite, late schizont, late trophozoite, Oocyst. Otto TD PlasmoDB Zanghi G
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intra-erythrocytic - 48 hs, gametocyte, early schizont, early trophozoite, Sporozoite. Otto TD PlasmoDB Zanghi G
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile intra-erythrocytic - 40 hs. Otto TD
Show/Hide expression data references
  • Otto TD New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.
  • Lasonder E Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes. Molecular insight into sex-specific processes and translational repression.
  • Zanghi G A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection.
  • PlasmoDB Data on upregulation of P. falciparum genes in different life cycle stages, combined from several microarray experiments available in PlasmoDB

Orthologs

Ortholog group members (OG5_129437)

Species Accession Gene Product
Arabidopsis thaliana AT1G30480   DNA-damage-repair/toleration protein DRT111
Babesia bovis BBOV_IV009160   conserved hypothetical protein
Brugia malayi Bm1_36780   G-patch domain containing protein
Caenorhabditis elegans CELE_F58B3.7   Protein F58B3.7
Dictyostelium discoideum DDB_G0270450   RNA recognition motif-containing protein RRM
Drosophila melanogaster Dmel_CG17540   CG17540 gene product from transcript CG17540-RB
Echinococcus granulosus EgrG_000112500   splicing factor 45
Echinococcus multilocularis EmuJ_000112500   splicing factor 45
Homo sapiens ENSG00000134453   RNA binding motif protein 17
Loa Loa (eye worm) LOAG_03171   G-patch domain-containing protein
Mus musculus ENSMUSG00000037197   RNA binding motif protein 17
Neospora caninum NCLIV_051870   DNA repair enzyme, putative
Onchocerca volvulus OVOC4548  
Plasmodium berghei PBANKA_1317700   RNA-binding protein, putative
Plasmodium falciparum PF3D7_1454000   RNA-binding protein, putative
Plasmodium knowlesi PKNH_1228100   RNA-binding protein, putative
Plasmodium vivax PVX_117780   RNA-binding protein, putative
Plasmodium yoelii PY00795   G-patch domain, putative
Schistosoma japonicum Sjp_0309900   expressed protein
Schistosoma japonicum Sjp_0023820   Splicing factor 45, putative
Schistosoma mansoni Smp_161750   hypothetical protein
Schmidtea mediterranea mk4.001549.03   Splicing factor 45
Trypanosoma congolense TcIL3000_7_4190   hypothetical protein
Toxoplasma gondii TGME49_214820   G-patch domain-containing protein
Theileria parva TP01_0856   hypothetical protein

Essentiality

PF3D7_1454000 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
TGME49_214820 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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
  • 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
  • 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.
  • 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.
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database

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
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

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.

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Gene identifier PF3D7_1454000 (Plasmodium falciparum), RNA-binding protein, putative
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