Detailed view for PF3D7_1468800

Basic information

TDR Targets ID: 2986
Plasmodium falciparum, splicing factor U2AF large subunit, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 10.124 | Length (AA): 833 | MW (Da): 97428 | 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:0000398   nuclear mRNA splicing, via spliceosome  
GO:0005634   nucleus  
GO:0003723   RNA binding  
GO:0003676   nucleic acid binding  
GO:0000166   nucleotide binding  
GO:0006397   mRNA processing  

Metabolic Pathways

Spliceosome (KEGG)

Structural information

Modbase 3D models:

There are 13 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
454 545 2fzr (A) 147 229 41.00 0.0000000009 0.97 0.62 -1.37
458 671 1cvj (A) 13 179 22.00 0 1 0.26 -0.04
586 712 1fnx (H) 36 147 27.00 0.0000000000063 1 0.35 0.15
591 663 1oo0 (B) 75 147 26.00 0.0000042 1 0.6 -1.87
1 175 4uos (A) 8 182 15.00 0.015 0.01 0.505484 -1.94
456 666 3vaj (A) 149 336 46.00 0 1 0.540601 0.15
591 659 1hl6 (A) 75 144 30.00 0.026 1 0.578133 -1.13
725 825 2pe8 (A) 299 392 43.00 0.018 1 0.463549 0
728 830 3v4m (A) 373 474 32.00 0.0000000091 1 0.639649 -1.49
745 821 1jmt (A) 74 146 23.00 0.0084 0.57 0.306437 -0.3
1 174 4uos (A) 8 184 20.00 0.038 0.07 0.542984 -1.84
728 830 3v4m (A) 373 474 33.00 0.0000000072 1 0.646249 -1.47
756 830 2mkc (A) 26 99 20.00 0.32 0.76 0.224636 0.27

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 Male Gametocyte. Lasonder E
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, sporozoite, early ring, early schizont, early trophozoite, late ring, late trophozoite, Oocyst, Ring, Female Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 24 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, gametocyte, late schizont, Sporozoite. Otto TD PlasmoDB Zanghi G
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intra-erythrocytic - 32 hs. Otto TD
Show/Hide expression data references
  • Zanghi G A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection.
  • 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.
  • PlasmoDB Data on upregulation of P. falciparum genes in different life cycle stages, combined from several microarray experiments available in PlasmoDB

Orthologs

Ortholog group members (OG5_128315)

Species Accession Gene Product
Arabidopsis thaliana AT4G36690   Splicing factor U2af large subunit A
Arabidopsis thaliana AT1G60900   Splicing factor U2af large subunit B
Babesia bovis BBOV_II004960   RNA recognition motif (RRM)-containing protein
Brugia malayi Bm1_09760   U2 auxiliary factor 65 kDa subunit
Candida albicans CaO19.5828   similar to spliceosomal U2 snRNP auxilliary factor large subunit
Candida albicans CaO19.13250   similar to spliceosomal U2 snRNP auxilliary factor large subunit
Caenorhabditis elegans CELE_Y92C3B.2   Protein UAF-1, isoform B
Cryptosporidium hominis Chro.20162   U2 snRNP auxiliary factor
Cryptosporidium parvum cgd2_1480   splicing factor U2AF U2 SnRNP auxiliary factor large subunit, RRM domain
Dictyostelium discoideum DDB_G0286395   RNA recognition motif-containing protein RRM
Drosophila melanogaster Dmel_CG9998   U2 small nuclear riboprotein auxiliary factor 50
Echinococcus granulosus EgrG_000625400   U2 small nuclear RNA auxiliary factor 2
Echinococcus granulosus EgrG_000688300   U2 small nuclear ribonucleoprotein
Echinococcus granulosus EgrG_000688400   Splicing factor U2AF 50 kDa subunit
Entamoeba histolytica EHI_098300   U2 snRNP auxiliary factor large subunit, putative
Echinococcus multilocularis EmuJ_000688400   Splicing factor U2AF 50 kDa subunit
Echinococcus multilocularis EmuJ_000625400   U2 small nuclear RNA auxiliary factor 2
Echinococcus multilocularis EmuJ_000688300   U2 small nuclear ribonucleoprotein
Homo sapiens ENSG00000063244   U2 small nuclear RNA auxiliary factor 2
Loa Loa (eye worm) LOAG_05996   U2af splicing factor protein 1
Loa Loa (eye worm) LOAG_09095   U2af splicing factor protein 1
Mus musculus ENSMUSG00000030435   U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) 2
Mus musculus 102640468   splicing factor U2AF 65 kDa subunit-like
Neospora caninum NCLIV_043320   RNA recognition motif (RRM)-containing protein, related
Oryza sativa 4351124   Os11g0682300
Oryza sativa 4350981   Os11g0636900
Onchocerca volvulus OVOC9366   Splicing factor U2AF 65 kDa subunit homolog
Plasmodium berghei PBANKA_1332000   splicing factor U2AF large subunit, putative
Plasmodium falciparum PF3D7_1468800   splicing factor U2AF large subunit, putative
Plasmodium knowlesi PKNH_1212400   splicing factor U2AF large subunit, putative
Plasmodium vivax PVX_117025   splicing factor U2AF large subunit, putative
Plasmodium yoelii PY04361   splicing factor-like protein, putative
Schistosoma japonicum Sjp_0301420   similar to Splicing factor U2AF 65 kDa subunit, putative
Schistosoma japonicum Sjp_0219100   similar to Splicing factor U2AF 65 kDa subunit, putative
Schistosoma mansoni Smp_019690   splicing factor u2af large subunit
Schmidtea mediterranea mk4.002347.00   Splicing factor U2AF 65 kDa subunit
Schmidtea mediterranea mk4.002187.01   Splicing factor U2AF 65 kDa subunit
Schmidtea mediterranea mk4.000276.09   Splicing factor U2AF 65 kDa subunit
Schmidtea mediterranea mk4.000276.08   Splicing factor U2AF 65 kDa subunit
Schmidtea mediterranea mk4.000406.05   Splicing factor U2AF 65 kDa subunit
Schmidtea mediterranea mk4.000406.06   Splicing factor U2AF 65 kDa subunit
Toxoplasma gondii TGME49_291950   RNA recognition motif-containing protein
Toxoplasma gondii TGME49_234520   U2 snRNP auxilliary factor, large subunit, splicing factor subfamily protein
Theileria parva TP04_0035   U2 small nuclear ribonucleoprotein, auxiliary factor, large subunit, putative

Essentiality

PF3D7_1468800 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
CELE_Y92C3B.2 Caenorhabditis elegans embryonic arrest wormbase
CELE_Y92C3B.2 Caenorhabditis elegans embryonic lethal wormbase
CELE_Y92C3B.2 Caenorhabditis elegans larval arrest wormbase
CELE_Y92C3B.2 Caenorhabditis elegans larval lethal wormbase
CELE_Y92C3B.2 Caenorhabditis elegans slow growth wormbase
CELE_Y92C3B.2 Caenorhabditis elegans sterile wormbase
PBANKA_1332000 Plasmodium berghei Essential plasmo
TGME49_234520 Toxoplasma gondii Probably essential sidik
TGME49_291950 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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
  • 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
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930

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 PF3D7_1468800 (Plasmodium falciparum), splicing factor U2AF large subunit, putative
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