Detailed view for PVX_001060

Basic information

TDR Targets ID: 265453
Plasmodium vivax, splicing factor, putative
Source Database / ID:  PlasmoDB 

pI: 5.0671 | Length (AA): 724 | MW (Da): 88458 | 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

No Pfam domain information for this protein.

Gene Ontology

Mouse over links to read term descriptions.
GO:0005622   intracellular  
GO:0005515   protein binding  
GO:0005488   binding  
GO:0006396   RNA processing  

Metabolic Pathways

Spliceosome (KEGG)

Structural information

Modbase 3D models:

There are 11 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
37 165 2fo7 (A) 1 129 14.00 0 0.33 0.5 -1.6
69 152 1na3 (A) 2 85 15.00 0.0000000000031 0.77 0.57 -2.38
103 610 2gw1 (A) 97 606 12.00 0 0.99 0.79 0.11
2 115 1a17 (A) 27 140 16.00 0.00026 0.1 0.379559 -0.75
2 98 3vtx (A) 77 173 14.00 0.03 0.05 0.373078 -1.17
7 63 2fxm (B) 890 946 30.00 0.57 0.01 0.475529 -1.05
95 539 2ooe (A) 22 471 24.00 0.00000000019 1 0.671441 0.64
269 407 3bma (A) 241 359 38.00 0.45 0.67 0.170789 1.99
316 460 4h7y (A) 12 142 27.00 0.11 1 0.489076 -0.48
560 716 4uos (A) 25 183 18.00 0.25 0.23 0.356151 -0.57
685 717 4is1 (C) 473 505 6.00 0.45 0 0.30968 -2.27

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 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 - 40 hs, intraerythrocytic - 48 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_128090)

Species Accession Gene Product
Arabidopsis thaliana AT5G41770   putative crooked neck protein / cell cycle protein
Arabidopsis thaliana AT3G13210   putative crooked neck protein / cell cycle protein
Arabidopsis thaliana AT5G45990   putative crooked neck protein / cell cycle protein
Arabidopsis thaliana AT3G51110   Half-A-TPR repeat-containing protein
Babesia bovis BBOV_III004750   tetratricopeptide repeat domain containing protein
Brugia malayi Bm1_50550   Crooked neck-like protein 1
Candida albicans CaO19.7964   similar to factor involved in both pre-mRNA splicing and cell cycle progression
Candida albicans CaO19.332   similar to factor involved in both pre-mRNA splicing and cell cycle progression
Caenorhabditis elegans CELE_M03F8.3   Protein M03F8.3, isoform B
Cryptosporidium hominis Chro.70412   hypothetical protein
Cryptosporidium parvum cgd7_3690   crooked neck protein HAT repeats
Dictyostelium discoideum DDB_G0278819   HAT repeat-containing protein
Drosophila melanogaster Dmel_CG3193   crooked neck
Echinococcus granulosus EgrG_000844800   crooked neck pre mRNA splicing factor 1
Entamoeba histolytica EHI_175230   crooked neck protein, putative
Echinococcus multilocularis EmuJ_000844800   crooked neck pre mRNA splicing factor 1
Homo sapiens ENSG00000101343   crooked neck pre-mRNA splicing factor 1
Leishmania braziliensis LbrM.35.4530   hypothetical protein, conserved
Leishmania donovani LdBPK_364490.1   hypothetical protein, conserved
Leishmania infantum LinJ.36.4490   hypothetical protein, conserved
Leishmania major LmjF.36.4280   hypothetical protein, conserved
Leishmania mexicana LmxM.36.4280   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_03190   crooked neck
Mus musculus ENSMUSG00000001767   Crn, crooked neck-like 1 (Drosophila)
Neospora caninum NCLIV_037180   hypothetical protein
Oryza sativa 4338298   Os05g0289400
Oryza sativa 4348330   Os10g0328700
Oryza sativa 9268891   Os06g0523800
Plasmodium berghei PBANKA_1001400   pre-mRNA-splicing factor CLF1, putative
Plasmodium falciparum PF3D7_0403700   pre-mRNA-splicing factor CLF1, putative
Plasmodium knowlesi PKNH_0301700   pre-mRNA-splicing factor CLF1, putative
Plasmodium vivax PVX_001060   splicing factor, putative
Plasmodium yoelii PY02447   hypothetical protein
Saccharomyces cerevisiae YLR117C   Clf1p
Schistosoma japonicum Sjp_0048020   Crooked neck-like protein 1, putative
Schistosoma mansoni Smp_148230   Pre-mRNA-splicing factor CLF1
Schmidtea mediterranea mk4.007501.00   Crooked neck-like protein 1
Schmidtea mediterranea mk4.001551.03   Crooked neck-like protein 1
Trypanosoma brucei gambiense Tbg972.10.11820   hypothetical protein, conserved
Trypanosoma brucei Tb11.v5.0735   hypothetical protein, conserved
Trypanosoma brucei Tb927.10.9660   Splicing factor CRN, putative
Trypanosoma congolense TcIL3000_10_8690   HAT (Half-A-TPR) repeats, putative
Trypanosoma cruzi TcCLB.504147.320   hypothetical protein, conserved
Toxoplasma gondii TGME49_269200   crooked neck family 1 protein isoform 2, putative
Theileria parva TP02_0476   crooked neck protein, putative
Trichomonas vaginalis TVAG_139790   crooked neck protein, putative

Essentiality

PVX_001060 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.10.9660 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.10.9660 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.10.9660 Trypanosoma brucei significant gain of fitness in procyclic forms alsford
Tb927.10.9660 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_M03F8.3 Caenorhabditis elegans embryonic lethal wormbase
CELE_M03F8.3 Caenorhabditis elegans larval arrest wormbase
CELE_M03F8.3 Caenorhabditis elegans sterile wormbase
YLR117C Saccharomyces cerevisiae inviable yeastgenome
PBANKA_1001400 Plasmodium berghei Essential plasmo
TGME49_269200 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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.
  • 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
  • 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
  • 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
  • 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
  • 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.

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 PVX_001060 (Plasmodium vivax), splicing factor, putative
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