Detailed view for PVX_100690

Basic information

TDR Targets ID: 269595
Plasmodium vivax, splicing factor 3B subunit 3, putative
Source Database / ID:  PlasmoDB 

pI: 6.3537 | Length (AA): 1230 | MW (Da): 138771 | Paralog Number: 0

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

Druggability Group : DG5

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

PF03178   CPSF A subunit region
PF10433   Mono-functional DNA-alkylating methyl methanesulfonate N-term

Gene Ontology

Mouse over links to read term descriptions.
GO:0005634   nucleus  
GO:0005515   protein binding  
GO:0003676   nucleic acid binding  

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
1 1229 2b5l (A) 1 1139 21.00 0 1 0.95 0.02
1 1225 2b5l (A) 1 1136 23.00 0 1 1.17 -0.04
440 762 2b5n (A) 392 705 23.00 0 1 0.56 -0.47
1 1229 2b5l (A) 1 1139 22.00 0 1 1.04779 0.79
5 1225 2b5l (A) 5 1136 25.00 0 1 1.05678 0.96

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 60-80% percentile intraerythrocytic - 6 hs, intraerythrocytic - 12 hs, intraerythrocytic - 18 hs, intraerythrocytic - 24 hs. Zhu L
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intraerythrocytic - 30 hs, intraerythrocytic - 36 hs, intraerythrocytic - 48 hs. Zhu L
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intraerythrocytic - 40 hs. Zhu L
Show/Hide expression data references
  • Zhu L New insights into the Plasmodium vivax transcriptome using RNA-Seq.

Orthologs

Ortholog group members (OG5_128558)

Species Accession Gene Product
Arabidopsis thaliana AT3G55220   spliceosome-associated protein 130B
Arabidopsis thaliana AT3G55200   spliceosomal associated protein 130A
Babesia bovis BBOV_II004270   splicing factor 3b, subunit 3, 130kD, putative
Brugia malayi Bm1_19455   splicing factor 3B subunit 3
Candida albicans CaO19.12846   similar to U2 snRNP complex splicing factor SF3b subunit SAP130 and to S. cerevisiae RSE1 (YML049C)
Candida albicans CaO19.5391   similar to U2 snRNP complex splicing factor SF3b subunit SAP130 and to S. cerevisiae RSE1 (YML049C)
Caenorhabditis elegans CELE_K02F2.3   Protein TEG-4
Cryptosporidium hominis Chro.80487   CG13900 gene product
Cryptosporidium parvum cgd8_4240   possible spliceosome factor
Dictyostelium discoideum DDB_G0282569   CPSF domain-containing protein
Drosophila melanogaster Dmel_CG13900   CG13900 gene product from transcript CG13900-RA
Echinococcus granulosus EgrG_000633300   splicing factor 3b subunit 3
Entamoeba histolytica EHI_144720   CPSF A subunit region protein, putative
Echinococcus multilocularis EmuJ_000633300   splicing factor 3b subunit 3
Homo sapiens ENSG00000189091   splicing factor 3b, subunit 3, 130kDa
Loa Loa (eye worm) LOAG_03297   hypothetical protein
Mus musculus ENSMUSG00000033732   splicing factor 3b, subunit 3
Neospora caninum NCLIV_031340   Splicing factor 3B subunit 3, putative
Oryza sativa 4328237   Os02g0137400
Onchocerca volvulus OVOC11814  
Plasmodium berghei PBANKA_1449400   splicing factor 3B subunit 3, putative
Plasmodium falciparum PF3D7_1234800   splicing factor 3B subunit 3, putative
Plasmodium knowlesi PKNH_1454200   splicing factor 3B subunit 3, putative
Plasmodium vivax PVX_100690   splicing factor 3B subunit 3, putative
Plasmodium yoelii PY03514   Drosophila melanogaster CG13900 gene product
Saccharomyces cerevisiae YML049C   Rse1p
Schistosoma japonicum Sjp_0025810   Splicing factor 3B subunit 3, putative
Schmidtea mediterranea mk4.018922.00   Splicing factor 3B subunit 3
Schmidtea mediterranea mk4.043164.00   Splicing factor 3B subunit 3
Schmidtea mediterranea mk4.039880.00   Splicing factor 3B subunit 3
Schmidtea mediterranea mk4.005874.00   Splicing factor 3B subunit 3
Schmidtea mediterranea mk4.039880.01   Splicing factor 3B subunit 3
Toxoplasma gondii TGME49_230960   splicing factor 3b, subunit 3, putative
Theileria parva TP04_0182   hypothetical protein
Trichomonas vaginalis TVAG_013050   spliceosomal protein sap, putative

Essentiality

PVX_100690 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
CELE_K02F2.3 Caenorhabditis elegans embryonic lethal wormbase
CELE_K02F2.3 Caenorhabditis elegans larval arrest wormbase
CELE_K02F2.3 Caenorhabditis elegans sterile wormbase
YML049C Saccharomyces cerevisiae inviable yeastgenome
PBANKA_1449400 Plasmodium berghei Essential plasmo
TGME49_230960 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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
  • 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.
  • 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
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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.
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan

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
Species Known druggable target Linked compounds Reference
Homo sapiens splicing factor 3b, subunit 3, 130kDa Compounds References
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets
Obtained from network model

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.0096 1 1
0.0028 0.806 0.5

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 PVX_100690 (Plasmodium vivax), splicing factor 3B subunit 3, putative
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