Detailed view for LmjF.36.3040

Basic information

TDR Targets ID: 23242
Leishmania major, pre-mRNA branch site protein p14, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 9.4073 | Length (AA): 183 | MW (Da): 20382 | 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:0003676   nucleic acid binding  
GO:0000166   nucleotide binding  

Metabolic Pathways

Spliceosome (KEGG)

Structural information

Modbase 3D models:

There are 9 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
48 169 1n52 (B) 18 140 21.00 0 1 0.95 -0.25
65 170 2f9d (A) 12 117 34.00 0 1 1.09 -1.17
70 156 1p1t (A) 16 103 30.00 0 1 0.98 -1.65
48 169 1n52 (B) 18 140 20.00 0.0000073 1 0.927467 -0.1
52 139 2myf (A) 0 79 33.00 0.0034 0.97 0.712474 0.28
65 178 3lqv (A) 14 125 32.00 0.0000000013 1 1.08175 -0.58
67 125 4qpt (A) 376 432 23.00 0 0.99 0.682204 -0.79
67 143 2ywk (A) 7 83 25.00 0 1 0.828565 -1.24
134 183 5hmo (A) 812 861 26.00 0.26 0.05 0.643024 -1.14

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 amastigotes, metacyclic. Fernandes MC
Show/Hide expression data references
  • Fernandes MC Dual Transcriptome Profiling of Leishmania-Infected Human Macrophages Reveals Distinct Reprogramming Signatures.

Orthologs

Ortholog group members (OG5_128783)

Species Accession Gene Product
Arabidopsis thaliana AT5G12190   RNA-binding (RRM/RBD/RNP motifs) family protein
Babesia bovis BBOV_II005820   pre-mRNA branch site protein p14, putative
Candida albicans CaO19.6989   similar to spliceosomal protein SF3b p14
Caenorhabditis elegans CELE_C50D2.5   Protein C50D2.5
Cryptosporidium parvum cgd3_2310   hypothetical protein
Dictyostelium discoideum DDB_G0286297   RNA recognition motif-containing protein RRM
Drosophila melanogaster Dmel_CG13298   CG13298 gene product from transcript CG13298-RA
Echinococcus granulosus EgrG_000202800   14 kda subunit splicing factor 3b
Echinococcus multilocularis EmuJ_000202800   14 kda subunit splicing factor 3b
Homo sapiens ENSG00000115128   splicing factor 3b, subunit 6, 14kDa
Leishmania braziliensis LbrM.35.3260   pre-mRNA branch site protein p14, putative
Leishmania donovani LdBPK_363190.1   pre-mRNA branch site protein p14, putative
Leishmania infantum LinJ.36.3190   pre-mRNA branch site protein p14, putative
Leishmania major LmjF.36.3040   pre-mRNA branch site protein p14, putative
Leishmania mexicana LmxM.36.3040   pre-mRNA branch site protein p14, putative
Loa Loa (eye worm) LOAG_04189   hypothetical protein
Mus musculus ENSMUSG00000037361   splicing factor 3B, subunit 6
Neospora caninum NCLIV_001260   RNA binding protein, putative
Oryza sativa 4334543   Os03g0811700
Plasmodium berghei PBANKA_1439800   splicing factor 3B subunit 6, putative
Plasmodium falciparum PF3D7_1224900   splicing factor 3B subunit 6, putative
Plasmodium knowlesi PKNH_1444200   splicing factor 3B subunit 6, putative
Plasmodium vivax PVX_123875   splicing factor 3B subunit 6, putative
Plasmodium yoelii PY07239   Drosophila melanogaster RE19804p-related
Schistosoma japonicum Sjp_0071370   Pre-mRNA branch site p14-like protein, putative
Schistosoma mansoni Smp_032060   hypothetical protein
Schmidtea mediterranea mk4.001575.03   Splicing factor 3B subunit 6-like protein
Schmidtea mediterranea mk4.000177.13   Splicing factor 3B subunit 6-like protein
Schmidtea mediterranea mk4.000689.13   Splicing factor 3B subunit 6-like protein
Trypanosoma brucei gambiense Tbg972.10.9150   RNA-binding protein, putative,RBP15
Trypanosoma brucei Tb927.10.7470   RNA-binding protein, putative
Trypanosoma congolense TcIL3000_10_6430   RNA-binding protein, putative
Trypanosoma cruzi TcCLB.510105.33   RNA-binding protein, putative
Trypanosoma cruzi TcCLB.509715.23   RNA-binding protein, putative
Toxoplasma gondii TGME49_305010   pre-mRNA branch site protein p14, putative
Theileria parva TP02_0539   hypothetical protein, conserved
Trichomonas vaginalis TVAG_424320   spbc29a3.07C protein, putative

Essentiality

LmjF.36.3040 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.10.7470 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.10.7470 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.10.7470 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.10.7470 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
TGME49_305010 Toxoplasma gondii Probably non-essential sidik
Show/Hide essentiality data references
  • 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.
  • 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
  • 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
  • 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
  • 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.

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User comments

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Gene identifier LmjF.36.3040 (Leishmania major), pre-mRNA branch site protein p14, putative
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