Detailed view for Smp_170230

Basic information

TDR Targets ID: 287595
Schistosoma mansoni, rna recognition motif containing protein
Source Database / ID:  GeneDB

pI: 10.2931 | Length (AA): 279 | MW (Da): 32245 | 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

PF00076   RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)

Gene Ontology

Mouse over links to read term descriptions.
GO:0003676   nucleic acid binding  
GO:0000166   nucleotide binding  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in KEGG.

Structural information

Modbase 3D models:

There are 6 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
4 139 3pgw (S) 41 183 29.00 0.000000028 1 0.770155 0.34
22 162 1h2t (Z) 6 144 24.00 0 1 0.869476 -0.68
49 165 2mkc (A) 2 115 48.00 0 1 1.06745 -1.24
58 231 4f02 (A) 11 184 28.00 0 1 0.971356 -0.61
60 116 2dh8 (A) 12 70 44.00 0.0000041 1 0.735501 -0.3
175 227 5szg (B) 1892 1956 19.00 0 0.01 0.672064 -3.21

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_128283)

Species Accession Gene Product
Arabidopsis thaliana AT3G47120   RNA recognition motif and zinc finger domain-containing protein
Babesia bovis BBOV_IV005060   RNA-binding protein, putative
Brugia malayi Bm1_02690   RNA binding motif protein
Brugia malayi Bm1_24695   hypothetical protein
Candida albicans CaO19.8647   RRM-containing orf similar to S. cerevisiae YIR005W
Candida albicans CaO19.1045   RRM-containing orf similar to S. cerevisiae YIR005W
Caenorhabditis elegans CELE_C30B5.4   Protein C30B5.4
Cryptosporidium parvum cgd6_3490   RNA-binding protein, putative
Dictyostelium discoideum DDB_G0294559   RNA recognition motif-containing protein RRM
Drosophila melanogaster Dmel_CG10466   CG10466 gene product from transcript CG10466-RB
Echinococcus granulosus EgrG_000667300   RNA binding motif protein 2
Entamoeba histolytica EHI_169910   RNA recognition motif domain containing protein
Echinococcus multilocularis EmuJ_000667300   RNA binding motif protein 2
Homo sapiens ENSG00000134597   RNA binding motif protein, X-linked 2
Leishmania braziliensis LbrM.26.0770   hypothetical protein, conserved
Leishmania donovani LdBPK_260730.1   RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain), putative
Leishmania infantum LinJ.26.0730   hypothetical protein, conserved
Leishmania major LmjF.26.0760   hypothetical protein, conserved
Leishmania mexicana LmxM.26.0760   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_03303   hypothetical protein
Mus musculus ENSMUSG00000031107   RNA binding motif protein, X-linked 2
Neospora caninum NCLIV_024340   hypothetical protein
Oryza sativa 4334639   Os03g0826400
Plasmodium berghei PBANKA_0805800   RNA-binding protein, putative
Plasmodium falciparum PF3D7_0319500   RNA-binding protein, putative
Plasmodium knowlesi PKNH_0821700   RNA-binding protein, putative
Plasmodium vivax PVX_095260   RNA-binding protein, putative
Plasmodium yoelii PY00973   RNA recognition motif, putative
Saccharomyces cerevisiae YIR005W   Ist3p
Schistosoma japonicum Sjp_0109550   RNA-binding motif protein, X-linked 2, putative
Schistosoma mansoni Smp_170230   rna recognition motif containing protein
Schmidtea mediterranea mk4.001427.01   RNA-binding motif protein, X-linked 2
Trypanosoma brucei gambiense Tbg972.7.1150   RNA-binding protein, putative
Trypanosoma brucei Tb927.7.1180   RNA-binding protein, putative
Trypanosoma congolense TcIL3000_7_830   RNA-binding protein, putative
Trypanosoma cruzi TcCLB.508213.20   hypothetical protein, conserved
Trypanosoma cruzi TcCLB.507515.60   hypothetical protein, conserved
Toxoplasma gondii TGME49_263595   RNA-binding protein
Theileria parva TP01_0238   RNA-binding protein, putative
Trichomonas vaginalis TVAG_365450   RNA recognition motif containing protein, putative

Essentiality

Smp_170230 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.7.1180 Trypanosoma brucei significant gain of fitness in bloodstream forms (3 days) alsford
Tb927.7.1180 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.7.1180 Trypanosoma brucei significant gain of fitness in procyclic forms alsford
Tb927.7.1180 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_C30B5.4 Caenorhabditis elegans embryonic lethal wormbase
CELE_C30B5.4 Caenorhabditis elegans larval arrest wormbase
CELE_C30B5.4 Caenorhabditis elegans sterile wormbase
PBANKA_0805800 Plasmodium berghei Essential plasmo
TGME49_263595 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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.
  • 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.
  • 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
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84

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 Smp_170230 (Schistosoma mansoni), rna recognition motif containing protein
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