Detailed view for PF3D7_1235900

Basic information

TDR Targets ID: 829764
Plasmodium falciparum, pre-mRNA-splicing factor SYF1, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 6.0457 | Length (AA): 1031 | MW (Da): 125427 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | Predicted trans-membrane segments: 1

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

No Pfam domain information for this protein.

Gene Ontology

Mouse over links to read term descriptions.
GO:0005515   protein binding  
GO:0006396   RNA processing  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in 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
27 804 3s5h (A) 142 1010 23.00 0.63 0.97 0.663007 1.78
950 1016 2avp (A) 2 68 9.00 0.00007 0.01 0.255385 -1.17
962 1029 2pl2 (A) 155 221 10.00 0.58 0.02 0.225355 -0.85
16 213 4tql (A) 17 216 12.00 0.61 0.01 0.279452 -0.02
576 672 2wqh (A) 17 107 22.00 0.28 1 0.36715 -0.66

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 Ring. Zanghi G
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 8 hs, intra-erythrocytic - 24 hs, Oocyst, Male Gametocyte. Otto TD Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 16 hs, intra-erythrocytic - 32 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, Female Gametocyte. Otto TD Lasonder E
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile Sporozoite. Zanghi G
Show/Hide expression data references
  • 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_128360)

Species Accession Gene Product
Arabidopsis thaliana AT5G28740   tetratricopeptide repeat domain-containing protein
Babesia bovis BBOV_IV000660   XBA-binding protein 2, putative
Brugia malayi Bm1_33965   XPA-binding protein 2
Candida albicans CaO19.10411   RNA splicing
Candida albicans CaO19.2893   RNA splicing
Caenorhabditis elegans CELE_C50F2.3   Protein C50F2.3
Cryptosporidium hominis Chro.70121   ENSANGP00000023353
Cryptosporidium parvum cgd7_970   Syf1p. protein with 8 HAT domains
Dictyostelium discoideum DDB_G0277977   TPR-like helical domain-containing protein
Drosophila melanogaster Dmel_CG6197   CG6197 gene product from transcript CG6197-RA
Echinococcus granulosus EgrG_000237200   pre mRNA splicing factor SYF1
Entamoeba histolytica EHI_073290   hypothetical protein
Entamoeba histolytica EHI_073300   hypothetical protein, conserved
Echinococcus multilocularis EmuJ_000237200   pre mRNA splicing factor SYF1
Homo sapiens ENSG00000076924   XPA binding protein 2
Leishmania braziliensis LbrM.23.1790   hypothetical protein, conserved
Leishmania donovani LdBPK_231950.1   hypothetical protein, conserved
Leishmania infantum LinJ.23.1950   hypothetical protein, conserved
Leishmania major LmjF.23.1550   hypothetical protein, conserved
Leishmania mexicana LmxM.23.1550   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_08885   hypothetical protein
Loa Loa (eye worm) LOAG_16272   hypothetical protein
Loa Loa (eye worm) LOAG_08304   XPA-binding protein 2
Mus musculus ENSMUSG00000019470   XPA binding protein 2
Neospora caninum NCLIV_001120   XPA-binding protein, putative
Oryza sativa 4344088   Os07g0644300
Plasmodium berghei PBANKA_1450500   pre-mRNA-splicing factor SYF1, putative
Plasmodium falciparum PF3D7_1235900   pre-mRNA-splicing factor SYF1, putative
Plasmodium knowlesi PKNH_1455600   pre-mRNA-splicing factor SYF1, putative
Plasmodium vivax PVX_100745   pre-mRNA-splicing factor SYF1, putative
Plasmodium yoelii PY00967   Homo sapiens KIAA1177 protein
Saccharomyces cerevisiae YDR416W   Syf1p
Schistosoma japonicum Sjp_0071210   Pre-mRNA-splicing factor SYF1, putative
Schistosoma mansoni Smp_166240   hcnp homolog
Schmidtea mediterranea mk4.003962.01   Pre-mRNA-splicing factor SYF1
Schmidtea mediterranea mk4.003190.01   Pre-mRNA-splicing factor SYF1
Schmidtea mediterranea mk4.011985.00   Pre-mRNA-splicing factor SYF1
Trypanosoma brucei gambiense Tbg972.5.1840   hypothetical protein, conserved
Trypanosoma brucei Tb927.5.1340   pre-mRNA splicing factor, putative
Trypanosoma brucei Tb11.v5.0884   hypothetical protein, conserved
Trypanosoma congolense TcIL3000_0_29970   HAT (Half-A-TPR) repeats, putative
Trypanosoma congolense TcIL3000_5_1380   HAT (Half-A-TPR) repeats, putative
Trypanosoma cruzi TcCLB.509601.40   pre-mRNA splicing factor, putative
Trypanosoma cruzi TcCLB.509767.40   pre-mRNA splicing factor, putative
Toxoplasma gondii TGME49_305240   XPA binding protein 2 family protein
Theileria parva TP01_0087   adapter protein, putative
Trichomonas vaginalis TVAG_258450   pre-mRNA splicing factor, putative

Essentiality

PF3D7_1235900 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.5.1340 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.5.1340 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.5.1340 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.5.1340 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_C50F2.3 Caenorhabditis elegans embryonic lethal wormbase
CELE_C50F2.3 Caenorhabditis elegans larval arrest wormbase
CELE_C50F2.3 Caenorhabditis elegans larval lethal wormbase
CELE_C50F2.3 Caenorhabditis elegans slow growth wormbase
CELE_C50F2.3 Caenorhabditis elegans sterile wormbase
YDR416W Saccharomyces cerevisiae inviable yeastgenome
PBANKA_1450500 Plasmodium berghei Essential plasmo
TGME49_305240 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
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • 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.

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User comments

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Gene identifier PF3D7_1235900 (Plasmodium falciparum), pre-mRNA-splicing factor SYF1, putative
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