Detailed view for PF3D7_1030000

Basic information

TDR Targets ID: 1367
Plasmodium falciparum, transcription elongation factor SPT4, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 9.1793 | Length (AA): 133 | MW (Da): 15178 | 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

PF06093   Spt4/RpoE2 zinc finger

Gene Ontology

Mouse over links to read term descriptions.
GO:0032786   positive regulation of RNA elongation  
GO:0006355   regulation of transcription, DNA-dependent  
GO:0005634   nucleus  
GO:0008270   zinc ion binding  
GO:0008159   positive transcription elongation factor activity  
GO:0003700   transcription factor activity  
GO:0003682   chromatin binding  
GO:0045941   positive regulation of transcription  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 3 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
42 118 1ryq (A) 0 60 27.00 0 0.7 0.46 0.3
34 131 3h7h (A) 4 103 41.00 0 1 1.27604 -0.57
42 133 2exu (A) 3 93 32.00 0 1 0.932129 -0.6

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 - 0 hs, intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, intra-erythrocytic - 24 hs, intra-erythrocytic - 32 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, merozoite, sporozoite, Oocyst, Ring, Sporozoite, Female Gametocyte, Male Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile early ring, early trophozoite, late ring. PlasmoDB
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile early schizont, late trophozoite. PlasmoDB
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile late schizont. PlasmoDB
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
  • Zanghi G A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection.
  • Otto TD New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.
  • Lasonder E Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes. Molecular insight into sex-specific processes and translational repression.

Orthologs

Ortholog group members (OG5_128605)

Species Accession Gene Product
Arabidopsis thaliana AT5G08565   transcription elongation factor SPT4-1
Arabidopsis thaliana AT5G63670   transcription elongation factor SPT4-2
Babesia bovis BBOV_I002950   transcription factor, putative
Brugia malayi Bm1_28880   Transcription initiation protein SPT4 homolog 1, putative
Candida albicans CaO19.3947   Zn-finger protein
Candida albicans CaO19.11429   Zn-finger protein
Caenorhabditis elegans CELE_F54C4.2   Protein SPT-4
Cryptosporidium parvum cgd2_2820   transcription factor, putative
Dictyostelium discoideum DDB_G0285293   transcription initiation factor Spt4
Drosophila melanogaster Dmel_CG12372   CG12372 gene product from transcript CG12372-RA
Echinococcus granulosus EgrG_000232500   transcription elongation factor spt4
Entamoeba histolytica EHI_148350   transcription initiation protein SPT4, putative
Echinococcus multilocularis EmuJ_000232500   transcription elongation factor spt4
Homo sapiens ENSG00000213246   suppressor of Ty 4 homolog 1 (S. cerevisiae)
Loa Loa (eye worm) LOAG_04253   transcription elongation factor SPT4
Mus musculus ENSMUSG00000020485   suppressor of Ty 4A
Mus musculus 100041294   predicted gene 3258
Neospora caninum NCLIV_026170   hypothetical protein
Oryza sativa 4343956   Os07g0623400
Plasmodium berghei PBANKA_0514000   transcription elongation factor SPT4, putative
Plasmodium falciparum PF3D7_1030000   transcription elongation factor SPT4, putative
Plasmodium knowlesi PKNH_0614700   transcription elongation factor SPT4, putative
Plasmodium vivax PVX_111225   transcription elongation factor SPT4, putative
Plasmodium yoelii PY04106   transcription initiation protein spt4 homolog 1-related
Saccharomyces cerevisiae YGR063C   transcription elongation factor SPT4
Schistosoma japonicum Sjp_0208960   Transcription elongation factor SPT4, putative
Schistosoma mansoni Smp_012530.2   transcription elongation factor SPT4-like protein
Schmidtea mediterranea mk4.011221.00   Transcription elongation factor SPT4
Schmidtea mediterranea mk4.011101.00   Transcription elongation factor SPT4
Toxoplasma gondii TGME49_261220   transcription elongation factor SPT4
Theileria parva TP01_0543   transcription factor, putative
Trichomonas vaginalis TVAG_107370   suppressor of ty, putative

Essentiality

PF3D7_1030000 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
CELE_F54C4.2 Caenorhabditis elegans embryonic arrest wormbase
PBANKA_0514000 Plasmodium berghei Essential plasmo
TGME49_261220 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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
  • 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
  • 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.
  • 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
  • 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.

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_1030000 (Plasmodium falciparum), transcription elongation factor SPT4, putative
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