Detailed view for PF3D7_1357700

Basic information

TDR Targets ID: 2287
Plasmodium falciparum, U3 small nucleolar RNA-associated protein 21, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 6.3264 | Length (AA): 1218 | MW (Da): 143360 | 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

PF04192   Utp21 specific WD40 associated putative domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0032040   small subunit processome  
GO:0006364   rRNA processing  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 7 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
105 415 1erj (A) 318 707 7.00 0 0.39 0.28 -0.4
169 477 1sq9 (A) 13 332 11.00 0.000000041 0.98 0.26 0.3
158 343 4ux7 (A) 51 238 17.00 0.045 0.17 0.287809 -0.26
305 917 4nsx (A) 134 682 21.00 0 1 0.447384 1.08
309 892 4nsx (A) 141 657 24.00 0.00000017 1 0.445175 1.02
848 1016 2ab5 (A) 352 512 30.00 0.16 0.05 0.0764521 1.55
305 917 4nsx (A) 134 682 21.00 0 1 0.436584 1.19

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

Orthologs

Ortholog group members (OG5_128050)

Species Accession Gene Product
Arabidopsis thaliana AT4G04940   transducin/WD40 domain-containing protein
Babesia bovis BBOV_IV005020   WD domain, G-beta repeat containing protein
Brugia malayi Bm1_33435   Utp21 specific WD40 associated domain containing protein
Candida albicans CaO19.1566   similar to U3 snoRNP protein UTP21
Candida albicans CaO19.9139   similar to U3 snoRNP protein UTP21
Caenorhabditis elegans CELE_Y45F10D.7   Protein Y45F10D.7
Cryptosporidium hominis Chro.10322   WD-repeat membrane protein
Cryptosporidium parvum cgd1_2890   beta transducin ortholog with WD40 repeats
Dictyostelium discoideum DDB_G0277019   U3 small nucleolar ribonucleoprotein
Drosophila melanogaster Dmel_CG9799   CG9799 gene product from transcript CG9799-RA
Echinococcus granulosus EgrG_000162500   WD repeat containing protein 36
Entamoeba histolytica EHI_001960   WD domain containing protein
Echinococcus multilocularis EmuJ_000162500   WD repeat containing protein 36
Homo sapiens ENSG00000134987   WD repeat domain 36
Leishmania braziliensis LbrM.35.4460   hypothetical protein, conserved
Leishmania donovani LdBPK_364420.1   WD domain, G-beta repeat/Utp21 specific WD40 associated putative domain containing protein, putative
Leishmania infantum LinJ.36.4420   hypothetical protein, conserved
Leishmania major LmjF.36.4210   hypothetical protein, conserved
Leishmania mexicana LmxM.36.4210   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_03852   hypothetical protein
Loa Loa (eye worm) LOAG_03853   hypothetical protein
Mus musculus ENSMUSG00000038299   WD repeat domain 36
Neospora caninum NCLIV_036760   hypothetical protein
Oryza sativa 9270402   Os06g0644600
Plasmodium berghei PBANKA_1134000   U3 small nucleolar RNA-associated protein 21, putative
Plasmodium falciparum PF3D7_1357700   U3 small nucleolar RNA-associated protein 21, putative
Plasmodium knowlesi PKNH_1113800   U3 small nucleolar RNA-associated protein 21, putative
Plasmodium vivax PVX_114860   hypothetical protein, conserved
Plasmodium yoelii PY05885   hypothetical protein
Saccharomyces cerevisiae YLR409C   Utp21p
Schistosoma japonicum Sjp_0018490   WD repeat-containing protein 36, putative
Schistosoma japonicum Sjp_0310220   expressed protein
Schistosoma mansoni Smp_186640   hypothetical protein
Schistosoma mansoni Smp_168920   hypothetical protein
Schmidtea mediterranea mk4.001434.04   WD-repeat protein, putative
Schmidtea mediterranea mk4.001434.03   WD-repeat protein, putative
Trypanosoma brucei gambiense Tbg972.11.11750   hypothetical protein, conserved
Trypanosoma brucei Tb927.11.10480   PQQ-like domain/WD domain, G-beta repeat/Utp21 specific WD40 associated putative domain containing protein, putative
Trypanosoma congolense TcIL3000_0_58500   WD domain, G-beta repeat/Utp21 specific WD40 associated putative domain containing protein, putative
Trypanosoma congolense TcIL3000.11.11070   WD domain, G-beta repeat/Utp21 specific WD40 associated putative domain containing protein, putative
Trypanosoma cruzi TcCLB.510285.20   PQQ-like domain/WD domain, G-beta repeat/Utp21 specific WD40 associated putative domain containing protein, putative
Trypanosoma cruzi TcCLB.503823.130   PQQ-like domain/WD domain, G-beta repeat/Utp21 specific WD40 associated putative domain containing protein, putative
Toxoplasma gondii TGME49_269770   WD domain, G-beta repeat-containing protein
Theileria parva TP01_0242   hypothetical protein
Trichomonas vaginalis TVAG_489790   WD-repeat protein, putative
Trichomonas vaginalis TVAG_489780   conserved hypothetical protein

Essentiality

PF3D7_1357700 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb11.01.2250 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb11.01.2250 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb11.01.2250 Trypanosoma brucei significant gain of fitness in procyclic forms alsford
Tb11.01.2250 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_Y45F10D.7 Caenorhabditis elegans embryonic lethal wormbase
CELE_Y45F10D.7 Caenorhabditis elegans larval arrest wormbase
CELE_Y45F10D.7 Caenorhabditis elegans slow growth wormbase
CELE_Y45F10D.7 Caenorhabditis elegans sterile wormbase
YLR409C Saccharomyces cerevisiae inviable yeastgenome
PBANKA_1134000 Plasmodium berghei Essential plasmo
TGME49_269770 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.
  • 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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • 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

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 PF3D7_1357700 (Plasmodium falciparum), U3 small nucleolar RNA-associated protein 21, putative
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