Detailed view for PF3D7_0620500

Basic information

TDR Targets ID: 4557
Plasmodium falciparum, cleavage stimulation factor subunit 1, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 4.3721 | Length (AA): 650 | MW (Da): 76492 | 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

PF00400   WD domain, G-beta repeat

Gene Ontology

Mouse over links to read term descriptions.
GO:0005848   mRNA cleavage stimulating factor complex  
GO:0005515   protein binding  
GO:0003723   RNA 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 14 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
327 640 2h14 (A) 44 331 24.00 0 1 0.7 -0.1
340 549 1vyh (C) 196 408 25.00 0.0000019 0.97 0.57 0.08
424 556 2aq5 (A) 72 211 16.00 0.00000031 0.06 0.33 -0.07
425 641 1erj (A) 338 605 18.00 0 0.3 0.5 -0.21
2 115 4u5a (C) 103 239 22.00 0.35 0.09 0.403885 -0.85
266 551 4lg9 (A) 246 513 26.00 0.0000034 1 0.6337 0.71
286 603 3v7d (B) 332 704 23.00 0.000093 0.98 0.477931 1.04
452 615 5ch1 (A) 116 245 34.00 0.29 0.15 0.0860077 1.46
476 554 4pby (B) 226 307 34.00 0.071 0.95 0.522238 -0.61
498 586 4aow (A) 171 255 33.00 0.029 0.46 0.458623 0.09
31 116 3q8t (A) 175 263 21.00 0.051 0 0.3961 -1.05
247 554 4lg9 (A) 224 513 26.00 0.000002 1 0.692469 0.53
455 618 5ch1 (A) 116 245 34.00 0.27 0.15 0.0839485 1.46
479 557 4pby (B) 226 307 34.00 0.067 0.95 0.52078 -0.61

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 Oocyst, Ring. Zanghi G
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, intra-erythrocytic - 24 hs, intra-erythrocytic - 32 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, Female Gametocyte. Otto TD Lasonder E
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile Male Gametocyte. Lasonder E
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile Sporozoite. Zanghi G
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.
  • 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.

Orthologs

Ortholog group members (OG5_129724)

Species Accession Gene Product
Arabidopsis thaliana AT5G60940   transducin/WD40 domain-containing protein
Babesia bovis BBOV_II006860   WD domain, G-beta repeat containing protein
Brugia malayi Bm1_43290   Cleavage stimulation factor, 50 kDa subunit
Caenorhabditis elegans CELE_F28C6.3   Protein CPF-1
Cryptosporidium hominis Chro.40101   Cstf1-prov protein
Cryptosporidium parvum cgd4_820   WD repeat protein
Dictyostelium discoideum DDB_G0278769   WD40 repeat-containing protein
Drosophila melanogaster Dmel_CG2261   CG2261 gene product from transcript CG2261-RA
Echinococcus granulosus EgrG_000392300   cleavage stimulation factor subunit 1
Echinococcus multilocularis EmuJ_000392300   cleavage stimulation factor subunit 1
Homo sapiens 1477   cleavage stimulation factor, 3' pre-RNA, subunit 1, 50kDa
Leishmania braziliensis LbrM.33.0280   hypothetical protein, conserved
Leishmania donovani LdBPK_330300.1   hypothetical protein, conserved
Leishmania infantum LinJ.33.0300   hypothetical protein, conserved
Leishmania major LmjF.33.0280   hypothetical protein, conserved
Leishmania mexicana LmxM.32.0280   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_03033   cleavage stimulation factor
Mus musculus ENSMUSG00000027498   cleavage stimulation factor, 3' pre-RNA, subunit 1
Oryza sativa 4334149   Os03g0754900
Plasmodium berghei PBANKA_1119700   cleavage stimulation factor subunit 1, putative
Plasmodium falciparum PF3D7_0620500   cleavage stimulation factor subunit 1, putative
Plasmodium knowlesi PKNH_1129700   cleavage stimulation factor subunit 1, putative
Plasmodium vivax PVX_114150   cleavage stimulation factor subunit 1, putative
Plasmodium yoelii PY04225   hypothetical protein
Schistosoma japonicum Sjp_0209030   similar to Cleavage stimulation factor 50 kDa subunit, putative
Schistosoma mansoni Smp_045250   hypothetical protein
Schmidtea mediterranea mk4.001129.16   Cleavage stimulation factor subunit 1
Schmidtea mediterranea mk4.001129.10   Cleavage stimulation factor subunit 1
Trypanosoma brucei gambiense Tbg972.10.19280   hypothetical protein, conserved
Trypanosoma brucei Tb927.10.15740   hypothetical protein, conserved
Trypanosoma congolense TcIL3000_10_13520   WD domain, G-beta repeat, putative
Trypanosoma cruzi TcCLB.508899.30   hypothetical protein, conserved
Trypanosoma cruzi TcCLB.511365.10   hypothetical protein, conserved
Theileria parva TP02_0661   hypothetical protein

Essentiality

PF3D7_0620500 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.10.15740 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.10.15740 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.10.15740 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.10.15740 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_F28C6.3 Caenorhabditis elegans embryonic lethal wormbase
CELE_F28C6.3 Caenorhabditis elegans larval arrest wormbase
CELE_F28C6.3 Caenorhabditis elegans slow growth wormbase
PBANKA_1119700 Plasmodium berghei Slow plasmo
Show/Hide essentiality data references
  • 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
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection

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

Druggability index (range: 0 to 1): 0.5

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.

User comments

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Gene identifier PF3D7_0620500 (Plasmodium falciparum), cleavage stimulation factor subunit 1, putative
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