Detailed view for Smp_068420

Basic information

TDR Targets ID: 288178
Schistosoma mansoni, small nuclear ribonucleoprotein SM-D3
Source Database / ID:  GeneDB

pI: 11.8258 | Length (AA): 130 | MW (Da): 14207 | 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:0000387   spliceosomal snRNP biogenesis  
GO:0005681   spliceosome  
GO:0006396   RNA processing  

Metabolic Pathways

Spliceosome (KEGG)

Structural information

Modbase 3D models:

There is 1 model calculated for this protein. More info on this model, including the model itself is available at: Modbase

Target Beg Target End Template Template Beg Template End Identity Evalue Model Score MPQS zDope
1 84 4pjo (A) 1 84 74.00 0 1 1.59185 -1.16

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

No expression data available for this gene

Orthologs

Ortholog group members (OG5_127840)

Species Accession Gene Product
Arabidopsis thaliana AT1G76300   snRNP core protein SMD3
Arabidopsis thaliana AT1G20580   small nuclear ribonucleoprotein-like protein
Babesia bovis BBOV_II002410   small nuclear ribonucleoprotein (snRNP), putative
Brugia malayi Bm1_05810   small nuclear ribonucleoprotein Sm D3
Brugia malayi Bm1_18015   small nuclear ribonucleoprotein Sm D3
Brugia malayi Bm1_30490   small nuclear ribonucleoprotein Sm D3
Candida albicans CaO19.11622   snRNP core binding protein D3
Candida albicans CaO19.4146   snRNP core binding protein D3
Caenorhabditis elegans CELE_Y116A8C.42   Protein SNR-1
Cryptosporidium hominis Chro.10256   aspartyl protease-like
Cryptosporidium parvum cgd1_2250   small nucealr riboprotein SMD3, SM domain
Dictyostelium discoideum DDB_G0273003   LSM domain-containing protein
Drosophila melanogaster Dmel_CG8427   Small ribonucleoprotein particle protein SmD3
Echinococcus granulosus EgrG_000886700   small nuclear ribonucleoprotein sm d3
Entamoeba histolytica EHI_163710   LSM domain containing protein
Echinococcus multilocularis EmuJ_000886700   small nuclear ribonucleoprotein sm d3
Giardia lamblia GL50803_12164   Small nuclear ribonucleoprotein Sm D3, putative
Homo sapiens 6634   small nuclear ribonucleoprotein D3 polypeptide 18kDa
Leishmania braziliensis LbrM.20.3470   small nuclear ribonucleoprotein, putative
Leishmania donovani LdBPK_343670.1   small nuclear ribonucleoprotein sm d3
Leishmania infantum LinJ.34.3670   small nuclear ribonucleoprotein, putative
Leishmania major LmjF.34.3860   small nuclear ribonucleoprotein, putative
Leishmania mexicana LmxM.33.3860   small nuclear ribonucleoprotein, putative
Loa Loa (eye worm) LOAG_05334   small nuclear ribonucleoprotein Sm D3
Mus musculus 67332   small nuclear ribonucleoprotein D3
Neospora caninum NCLIV_053870   hypothetical protein
Oryza sativa 4327991   Os02g0102700
Oryza sativa 4332206   Os03g0240800
Plasmodium berghei PBANKA_0811000   small nuclear ribonucleoprotein Sm D3, putative
Plasmodium falciparum PF3D7_0909800   small nuclear ribonucleoprotein Sm D3, putative
Plasmodium knowlesi PKNH_0707800   small nuclear ribonucleoprotein Sm D3, putative
Plasmodium vivax PVX_098930   small nuclear ribonucleoprotein (snRNP), putative
Plasmodium yoelii PY03502   hypothetical protein
Saccharomyces cerevisiae YLR147C   Smd3p
Schistosoma japonicum Sjp_0201000   ko:K01173 endonuclease [EC3.1.30.-], putative
Schistosoma mansoni Smp_068420   small nuclear ribonucleoprotein SM-D3
Schmidtea mediterranea mk4.002460.02   Putative small nuclear ribonucleoprotein SM-D3
Schmidtea mediterranea mk4.000301.13   Putative small nuclear ribonucleoprotein SM-D3
Schmidtea mediterranea mk4.004208.01   Putative small nuclear ribonucleoprotein SM-D3
Trypanosoma brucei gambiense Tbg972.4.690   small nuclear ribonucleoprotein SmD3, putative
Trypanosoma brucei Tb927.4.890   small nuclear ribonucleoprotein sm d3
Trypanosoma congolense TcIL3000_4_490   small nuclear ribonucleoprotein sm d3
Trypanosoma cruzi TcCLB.508257.150   small nuclear ribonucleoprotein sm d3
Toxoplasma gondii TGME49_309740   LSM domain-containing protein
Theileria parva TP04_0358   small nuclear ribonucleoprotein, putative
Trichomonas vaginalis TVAG_260260   small nuclear ribonucleoprotein sm D3, putative
Trichomonas vaginalis TVAG_214100   small nuclear ribonucleoprotein sm, putative

Essentiality

Smp_068420 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.4.890 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.4.890 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.4.890 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.4.890 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_Y116A8C.42 Caenorhabditis elegans embryonic arrest wormbase
CELE_Y116A8C.42 Caenorhabditis elegans embryonic lethal wormbase
CELE_Y116A8C.42 Caenorhabditis elegans larval arrest wormbase
CELE_Y116A8C.42 Caenorhabditis elegans slow growth wormbase
CELE_Y116A8C.42 Caenorhabditis elegans sterile wormbase
YLR147C Saccharomyces cerevisiae inviable yeastgenome
TGME49_309740 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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
  • 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.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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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Gene identifier Smp_068420 (Schistosoma mansoni), small nuclear ribonucleoprotein SM-D3
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