Detailed view for PF3D7_0218700

Basic information

TDR Targets ID: 3449
Plasmodium falciparum, pre-mRNA-processing protein 45, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 9.8493 | Length (AA): 482 | MW (Da): 57526 | 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

PF02731   SKIP/SNW domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0008150   biological_process  
GO:0003674   molecular_function  
GO:0000398   nuclear mRNA splicing, via spliceosome  
GO:0005681   spliceosome  
GO:0005515   protein 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
22 466 3s5h (A) 462 999 16.00 0.0013 0.72 0.854537 0.98
125 253 3add (A) 111 233 32.00 0.69 0.04 0.444935 0.79
153 333 4uos (A) 1 183 21.00 0.14 0.14 0.648819 -1.25
240 389 1y4c (A) 313 641 17.00 0.52 0.14 0.354503 -0.05

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 - 8 hs, intra-erythrocytic - 16 hs, merozoite, sporozoite, early ring, early trophozoite, late ring, late trophozoite, Oocyst, Ring, Sporozoite, Male Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 24 hs, gametocyte, early schizont, late schizont, Female Gametocyte. Otto TD PlasmoDB Lasonder E
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 32 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs. Otto TD
Show/Hide expression data references
  • PlasmoDB Data on upregulation of P. falciparum genes in different life cycle stages, combined from several microarray experiments available in PlasmoDB
  • Zanghi G A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection.
  • 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.

Orthologs

Ortholog group members (OG5_128357)

Species Accession Gene Product
Arabidopsis thaliana AT1G77180   putative transcription factor SKIP
Babesia bovis BBOV_II005600   ski-interacting protein, putative
Brugia malayi Bm1_56860   Hypothetical 60.2 kDa protein T27F2.1 in chromosome V, putative
Candida albicans CaO19.12959   similar to N terminus of SkiP component of the spliceosome
Candida albicans CaO19.5513   similar to N terminus of SkiP component of the spliceosome
Caenorhabditis elegans CELE_T27F2.1   Protein SKP-1
Cryptosporidium hominis Chro.80502   Bx42 CG8264-PA
Cryptosporidium parvum cgd8_4380   SNW family nuclear protein
Dictyostelium discoideum DDB_G0269188   SKIP/SNW domain-containing protein
Drosophila melanogaster Dmel_CG8264   CG8264 gene product from transcript CG8264-RB
Echinococcus granulosus EgrG_000728000   SNW domain containing 1
Entamoeba histolytica EHI_199600   SKIP/SNW domain protein
Echinococcus multilocularis EmuJ_000728000   SNW domain containing 1
Homo sapiens ENSG00000100603   SNW domain containing 1
Leishmania braziliensis LbrM.15.1070   hypothetical protein, conserved
Leishmania donovani LdBPK_151090.1   SKIP/SNW domain containing protein, putative
Leishmania infantum LinJ.15.1090   hypothetical protein, conserved
Leishmania major LmjF.15.1030   hypothetical protein, conserved
Leishmania mexicana LmxM.15.1030   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_10368   SKP-1 protein
Mus musculus ENSMUSG00000021039   SNW domain containing 1
Neospora caninum NCLIV_033000   hypothetical protein, conserved
Oryza sativa 4330796   Os02g0759800
Onchocerca volvulus OVOC8353  
Onchocerca volvulus OVOC7200  
Onchocerca volvulus OVOC7709  
Onchocerca volvulus OVOC509  
Onchocerca volvulus OVOC10642  
Plasmodium berghei PBANKA_0315400   pre-mRNA-processing protein 45, putative
Plasmodium falciparum PF3D7_0218700   pre-mRNA-processing protein 45, putative
Plasmodium knowlesi PKNH_0402200   pre-mRNA-processing protein 45, putative
Plasmodium vivax PVX_002605   nuclear protein SkiP, putative
Plasmodium yoelii PY04746   chromatin-binding protein
Saccharomyces cerevisiae YAL032C   Prp45p
Schistosoma japonicum Sjp_0090120   ko:K06063 SKI interacting protein, putative
Schistosoma mansoni Smp_105860   nuclear protein SkiP
Schmidtea mediterranea mk4.002599.00   Puff-specific protein Bx42
Trypanosoma brucei gambiense Tbg972.9.3080   hypothetical protein, conserved
Trypanosoma brucei Tb927.9.5880   pre-mRNA splicing factor, putative
Trypanosoma congolense TcIL3000_9_1980   hypothetical protein, conserved
Trypanosoma cruzi TcCLB.509445.20   pre-mRNA splicing factor, putative
Toxoplasma gondii TGME49_233190   SKIP/SNW domain-containing protein
Theileria parva TP02_0511   hypothetical protein
Trichomonas vaginalis TVAG_402430   chromatin-binding protein, putative

Essentiality

PF3D7_0218700 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb09.160.4290 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb09.160.4290 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb09.160.4290 Trypanosoma brucei significant gain of fitness in procyclic forms alsford
Tb09.160.4290 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_T27F2.1 Caenorhabditis elegans embryonic lethal wormbase
CELE_T27F2.1 Caenorhabditis elegans larval arrest wormbase
CELE_T27F2.1 Caenorhabditis elegans sterile wormbase
YAL032C Saccharomyces cerevisiae inviable yeastgenome
PBANKA_0315400 Plasmodium berghei Essential plasmo
TGME49_233190 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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
  • 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.
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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.
  • 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_0218700 (Plasmodium falciparum), pre-mRNA-processing protein 45, putative
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