Detailed view for PF3D7_0109200

Basic information

TDR Targets ID: 3212
Plasmodium falciparum, cleavage and polyadenylation specificity factor subunit 5, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 9.6005 | Length (AA): 232 | MW (Da): 27319 | 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

PF13869   Nucleotide hydrolase

Gene Ontology

Mouse over links to read term descriptions.
GO:0006378   mRNA polyadenylation  
GO:0005849   mRNA cleavage factor complex  
GO:0003729   mRNA binding  

Metabolic Pathways

mRNA surveillance pathway (KEGG)

Structural information

Modbase 3D models:

There are 3 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
65 205 1ktg (A) 2 134 11.00 0 0.02 0.59 -0.43
2 221 3bho (A) 25 224 32.00 0 1 1.11808 0.04
59 177 1v8y (A) 27 152 12.00 0.000035 0.05 0.544531 0.84

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 intra-erythrocytic - 0 hs, intra-erythrocytic - 16 hs. Otto TD
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 8 hs, intra-erythrocytic - 24 hs, intra-erythrocytic - 32 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, Oocyst, Ring. Otto TD Zanghi G
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile gametocyte, early schizont, early trophozoite, late ring, late trophozoite, Female Gametocyte, Male Gametocyte. PlasmoDB Lasonder E
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile Sporozoite. Zanghi G
Show/Hide expression data references
  • Zanghi G A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection.
  • Otto TD New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.
  • PlasmoDB Data on upregulation of P. falciparum genes in different life cycle stages, combined from several microarray experiments available in PlasmoDB
  • Lasonder E Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes. Molecular insight into sex-specific processes and translational repression.

Orthologs

Ortholog group members (OG5_128813)

Species Accession Gene Product
Arabidopsis thaliana AT4G25550   cleavage/polyadenylation specificity factor
Babesia bovis BBOV_III007210   conserved hypothetical protein
Brugia malayi Bm1_28410   Pre-mrna cleavage factor, identical
Caenorhabditis elegans CELE_F43G9.5   Protein CFIM-1
Cryptosporidium hominis Chro.60436   hypothetical protein
Cryptosporidium parvum cgd6_3810   NUDIX domain protein; mRNA cleavage factor-like protein Im like, plant+animal group
Dictyostelium discoideum DDB_G0269370   NUDIX hydrolase family protein
Drosophila melanogaster Dmel_CG3689   CG3689 gene product from transcript CG3689-RB
Echinococcus granulosus EgrG_000088100   Cleavage and polyadenylation specificity factor
Entamoeba histolytica EHI_077110   hypothetical protein, conserved
Entamoeba histolytica EHI_077220   pre-mRNA cleavage factor I 25 kDa subunit, putative
Entamoeba histolytica EHI_077000   pre-mRNA cleavage factor I 25 kDa subunit, putative
Echinococcus multilocularis EmuJ_000088100   Cleavage and polyadenylation specificity factor
Homo sapiens ENSG00000167005   nudix (nucleoside diphosphate linked moiety X)-type motif 21
Leishmania braziliensis LbrM.26.0320   hypothetical protein, conserved
Leishmania donovani LdBPK_260280.1   nucleotide hydrolase, putative
Leishmania infantum LinJ.26.0280   hypothetical protein, conserved
Leishmania major LmjF.26.0290   hypothetical protein, conserved
Leishmania mexicana LmxM.26.0290   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_04228   pre-mRNA cleavage factor
Mus musculus 68219   nudix (nucleoside diphosphate linked moiety X)-type motif 21
Neospora caninum NCLIV_004770   hypothetical protein
Oryza sativa 4337444   Os04g0683100
Onchocerca volvulus OVOC1353   Cleavage and polyadenylation specificity factor subunit 5 homolog
Plasmodium berghei PBANKA_0204400   cleavage and polyadenylation specificity factor subunit 5, putative
Plasmodium falciparum PF3D7_0109200   cleavage and polyadenylation specificity factor subunit 5, putative
Plasmodium knowlesi PKNH_0204600   cleavage and polyadenylation specificity factor subunit 5, putative
Plasmodium vivax PVX_081325   mRNA cleavage factor-like protein, putative
Schistosoma japonicum Sjp_0217610   ko:K10636 autocrine motility factor receptor, putative
Schistosoma mansoni Smp_002190   pre-mRNA cleavage factor im 25kD subunit
Schmidtea mediterranea mk4.008959.02  
Schmidtea mediterranea mk4.003994.01   Cleavage and polyadenylation specificity factor subunit 5
Schmidtea mediterranea mk4.002056.06   Cleavage and polyadenylation specificity factor subunit 5
Trypanosoma brucei gambiense Tbg972.7.1630   hypothetical protein, conserved
Trypanosoma brucei Tb927.7.1620   Cleavage factor I 25 kDa subunit, putative
Trypanosoma congolense TcIL3000_7_1170   hypothetical protein, conserved
Trypanosoma cruzi TcCLB.509509.40   hypothetical protein, conserved
Trypanosoma cruzi TcCLB.508207.220   hypothetical protein, conserved
Toxoplasma gondii TGME49_221190   mrna cleavage factor family protein, putative
Theileria parva TP04_0626   mRNA cleavage factor protein, putative
Trichomonas vaginalis TVAG_475950   pre-mRNA cleavage factor im, 25kD subunit, putative

Essentiality

PF3D7_0109200 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.7.1620 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.7.1620 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb927.7.1620 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.7.1620 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_F43G9.5 Caenorhabditis elegans embryonic lethal wormbase
CELE_F43G9.5 Caenorhabditis elegans larval arrest wormbase
CELE_F43G9.5 Caenorhabditis elegans sterile wormbase
TGME49_221190 Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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
  • 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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.

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User comments

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Gene identifier PF3D7_0109200 (Plasmodium falciparum), cleavage and polyadenylation specificity factor subunit 5, putative
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