Detailed view for PBANKA_1023200

Basic information

TDR Targets ID: 826843
Plasmodium berghei, splicing factor 3B subunit 4, putative
Source Database / ID: 

pI: 4.9682 | Length (AA): 424 | MW (Da): 47201 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | Predicted trans-membrane segments: 0

Druggability Group : DG

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  

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
14 103 5gvq (A) 9 98 49.00 0 1 0.883164 -0.9
16 244 5ca5 (A) 111 331 17.00 0 1 0.595594 0.54
22 101 1p27 (B) 74 153 29.00 0 1 0.642179 -1.31
110 155 2dh8 (A) 12 58 33.00 0.16 1 0.556391 -0.47

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 4 hs Ring, Erthyrocytic stages. Otto TD Yeoh LM
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile Gametocyte, 16 hs Trophozoite, 22 hs Schizont, Female gametocyte, Male gametocyte. Otto TD Yeoh LM
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile Ookinete. Otto TD
Show/Hide expression data references
  • Otto TD A comprehensive evaluation of rodent malaria parasite genomes and gene expression.
  • Yeoh LM Comparative transcriptomics of female and male gametocytes in Plasmodium berghei and the evolution of sex in alveolates.

Orthologs

Ortholog group members (OG5_128231)

Species Accession Gene Product
Arabidopsis thaliana AT2G18510   RNA-binding (RRM/RBD/RNP motifs) family protein
Babesia bovis BBOV_III006220   RNA recognition motif domaining containing protein
Brugia malayi Bm1_43460   Hypothetical RNA-binding protein C08B11.5 in chromosome II
Candida albicans CaO19.2261   similar to U2 snRNA-associated pre-mRNA splicing factor SAP49, S. cerevisiae HSH49 (YOR319W)
Candida albicans CaO19.9801   similar to U2 snRNA-associated pre-mRNA splicing factor SAP49, S. cerevisiae HSH49 (YOR319W)
Caenorhabditis elegans CELE_C08B11.5   Protein SAP-49
Cryptosporidium hominis Chro.60515   splicing factor
Cryptosporidium parvum cgd6_4490   U2 snRNP. Hsh49p, RRM domain containing protein
Dictyostelium discoideum DDB_G0267714   RNA recognition motif-containing protein RRM
Drosophila melanogaster Dmel_CG3780   Spliceosomal protein on the X
Echinococcus granulosus EgrG_000926950   splicing factor 3b subunit 4
Entamoeba histolytica EHI_012460   splicing factor 3B subunit 4, putative
Echinococcus multilocularis EmuJ_000926950   splicing factor 3b subunit 4
Giardia lamblia GL50803_25011   Splicing factor 3B subunit, putative
Homo sapiens ENSG00000143368   splicing factor 3b, subunit 4, 49kDa
Leishmania braziliensis LbrM.29.0330   RNA binding protein, putative
Leishmania donovani LdBPK_290400.1   RNA binding protein, putative
Leishmania infantum LinJ.29.0400   RNA binding protein, putative
Leishmania major LmjF.29.0390   RNA binding protein, putative
Leishmania mexicana LmxM.08_29.0390   RNA binding protein, putative
Loa Loa (eye worm) LOAG_01189   spliceosomal protein on the X
Mus musculus ENSMUSG00000068856   splicing factor 3b, subunit 4
Neospora caninum NCLIV_048140   splicing factor, putative
Oryza sativa 4348798   Os10g0457000
Onchocerca volvulus OVOC13482  
Plasmodium berghei PBANKA_1023200   splicing factor 3B subunit 4, putative
Plasmodium falciparum PF3D7_1420000   splicing factor 3B subunit 4, putative
Plasmodium knowlesi PKNH_1338000   splicing factor 3B subunit 4, putative
Plasmodium vivax PVX_085480   spliceosome-associated protein 49, putative
Plasmodium yoelii PY01202   splicing factor 3b subunit 4
Saccharomyces cerevisiae YOR319W   Hsh49p
Schistosoma japonicum Sjp_0031090   Splicing factor 3B subunit 4, putative
Schmidtea mediterranea mk4.037827.00   Splicing factor 3B subunit 4
Schmidtea mediterranea mk4.007289.00   Splicing factor 3B subunit 4
Trypanosoma brucei gambiense Tbg972.3.5980   RNA-binding protein, putative,spliceosome-associated protein, putative
Trypanosoma brucei Tb927.3.5280   spliceosome-associated protein 49, putative
Trypanosoma congolense TcIL3000_3_3220   spliceosome- associated protein, putative
Trypanosoma cruzi TcCLB.508409.270   RNA-binding protein, putative
Trypanosoma cruzi TcCLB.510143.80   RNA-binding protein, putative
Toxoplasma gondii TGME49_224580   RNA recognition motif-containing protein
Theileria parva TP02_0374   spliceosome associated protein, putative
Trichomonas vaginalis TVAG_245890   polyadenylate-binding protein, putative

Essentiality

PBANKA_1023200 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb927.3.5280 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.3.5280 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.3.5280 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.3.5280 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_C08B11.5 Caenorhabditis elegans embryonic arrest wormbase
CELE_C08B11.5 Caenorhabditis elegans embryonic lethal wormbase
CELE_C08B11.5 Caenorhabditis elegans slow growth wormbase
CELE_C08B11.5 Caenorhabditis elegans sterile wormbase
YOR319W Saccharomyces cerevisiae inviable yeastgenome
PBANKA_1023200 this record Plasmodium berghei Slow plasmo
TGME49_224580 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • 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
  • 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
  • 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924

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 PBANKA_1023200 (Plasmodium berghei), splicing factor 3B subunit 4, putative
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