Detailed view for PF3D7_1350200

Basic information

TDR Targets ID: 168
Plasmodium falciparum, small nuclear ribonucleoprotein E, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 9.8417 | Length (AA): 93 | MW (Da): 10927 | 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

PF01423   LSM domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0000398   nuclear mRNA splicing, via spliceosome  
GO:0005732   small nucleolar ribonucleoprotein complex  
GO:0005681   spliceosome  
GO:0006396   RNA processing  

Metabolic Pathways

Spliceosome (KEGG)

Structural information

Modbase 3D models:

There are 5 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
12 87 2fwk (A) 26 111 32.00 0 0.85 1.28 -1.45
13 89 1b34 (B) 26 113 25.00 0 0.75 1.13 -2.13
5 88 3pgw (E) 7 90 56.00 0 0.99 1.50913 0.42
30 86 3pgg (A) 40 110 37.00 0.000021 0.81 1.0476 -0.43
41 88 1i8f (A) 34 79 33.00 0.13 0.27 0.759829 0.64

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, intra-erythrocytic - 32 hs, Oocyst, Ring. Otto TD Zanghi G
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 24 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, Sporozoite, Female Gametocyte. Otto TD Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile Male Gametocyte. 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_128224)

Species Accession Gene Product
Arabidopsis thaliana AT4G30330   small nuclear ribonucleoprotein E
Babesia bovis BBOV_IV002640   small nuclear ribonucleoprotein E, putative
Brugia malayi Bm1_16025   small nuclear ribonucleoprotein E
Caenorhabditis elegans CELE_Y49E10.15   Protein SNR-6
Cryptosporidium parvum cgd4_1660   small nuclear ribonucleoprotein, putative
Dictyostelium discoideum DDB_G0302414   small nuclear ribonucleoprotein E
Drosophila melanogaster Dmel_CG18591   Small ribonucleoprotein particle protein SmE
Echinococcus granulosus EgrG_000181000   small nuclear ribonucleoprotein polypeptide
Entamoeba histolytica EHI_141910   LSM domain containing protein
Echinococcus multilocularis EmuJ_000181000   small nuclear ribonucleoprotein polypeptide
Homo sapiens 6635   small nuclear ribonucleoprotein polypeptide E
Leishmania braziliensis LbrM.30.1330   small nuclear ribonucleoprotein polypeptide e, putative
Leishmania donovani LdBPK_301270.1   small nuclear ribonucleoprotein polypeptide e, putative
Leishmania infantum LinJ.30.1270   small nuclear ribonucleoprotein polypeptide e, putative
Leishmania major LmjF.30.1205   small nuclear ribonucleoprotein polypeptide e, putative
Leishmania mexicana LmxM.29.1205   small nuclear ribonucleoprotein polypeptide e, putative
Loa Loa (eye worm) LOAG_06135   small nuclear ribonucleoprotein E
Mus musculus 102632439   predicted gene 14284
Mus musculus ENSMUSG00000090553   small nuclear ribonucleoprotein E
Neospora caninum NCLIV_007180   hypothetical protein
Oryza sativa 4328158   Os02g0126700
Plasmodium berghei PBANKA_1363000   small nuclear ribonucleoprotein E, putative
Plasmodium falciparum PF3D7_1350200   small nuclear ribonucleoprotein E, putative
Plasmodium knowlesi PKNH_1250700   small nuclear ribonucleoprotein E, putative
Plasmodium vivax PVX_083405   small nuclear ribonucleoprotein E, putative
Plasmodium yoelii PY05604   small nuclear ribonucleoprotein homolog
Saccharomyces cerevisiae YOR159C   Sme1p
Schistosoma japonicum Sjp_0103260   Small nuclear ribonucleoprotein E, putative
Trypanosoma brucei gambiense Tbg972.6.2470   small nuclear ribonucleoprotein Sm-E
Trypanosoma brucei Tb927.6.2700   small nuclear ribonucleoprotein Sm-E
Trypanosoma cruzi TcCLB.511499.59   small nuclear ribonucleoprotein Sm-E, putative
Trypanosoma cruzi TcCLB.509965.30   small nuclear ribonucleoprotein Sm-E, putative
Toxoplasma gondii TGME49_275750   small nuclear ribonucleoprotein E, putative
Theileria parva TP03_0386   small nuclear ribonucleoprotein, putative
Trichomonas vaginalis TVAG_473940   Small nuclear ribonucleoprotein E, putative

Essentiality

PF3D7_1350200 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.6.2700 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.6.2700 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.6.2700 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.6.2700 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_Y49E10.15 Caenorhabditis elegans embryonic arrest wormbase
CELE_Y49E10.15 Caenorhabditis elegans embryonic lethal wormbase
CELE_Y49E10.15 Caenorhabditis elegans larval arrest wormbase
CELE_Y49E10.15 Caenorhabditis elegans slow growth wormbase
CELE_Y49E10.15 Caenorhabditis elegans sterile wormbase
YOR159C Saccharomyces cerevisiae inviable yeastgenome
TGME49_275750 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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
  • 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
  • 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
  • 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

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.

User comments

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Gene identifier PF3D7_1350200 (Plasmodium falciparum), small nuclear ribonucleoprotein E, putative
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