Detailed view for Sjp_0011400

Basic information

TDR Targets ID: 967356
Schistosoma japonicum, Histone demethylase rbr-2, putative
Source Database / ID:  Wormbase Parasite  

pI: 7.6868 | Length (AA): 1968 | MW (Da): 223244 | Paralog Number: 2

Signal peptide: N | GPI Anchor: | Predicted trans-membrane segments: 0

Druggability Group : DG

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

PF00628   PHD-finger
PF01388   ARID/BRIGHT DNA binding domain
PF02373   JmjC domain, hydroxylase
PF02375   jmjN domain
PF02928   C5HC2 zinc finger
PF08429   PLU-1-like protein

Gene Ontology

Mouse over links to read term descriptions.
GO:0003677   DNA binding  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in 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
3 627 5a1f (A) 0 741 51.00 0 1 0.315943 1.67
4 653 5v9p (A) 12 781 47.00 0 1 0.700652 0.05
65 173 1kqq (A) 12 121 28.00 0 1 0.356414 -0.99
189 636 5fyz (A) 28 750 44.00 0 1 0.680058 -0.5
191 246 2mny (A) 307 360 56.00 0 0.98 0.48647 0.32
192 242 5vab (A) 21 69 45.00 0 1 0.482928 -0.79
373 489 3opt (A) 222 338 41.00 0 0.99 0.576681 -0.23
642 1501 2x1g (F) 28 925 12.00 0 0.99 0.374214 0.41
1719 1944 5cwp (A) 1 225 13.00 0.19 0.02 0.270496 -0.71

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

No expression data available for this gene

Orthologs

Ortholog group members (OG5_127370)

Species Accession Gene Product
Arabidopsis thaliana AT1G30810   jumonji domain-containing protein 18
Arabidopsis thaliana AT1G63490   transcription factor jumonji (jmjC) domain-containing protein
Arabidopsis thaliana AT1G08620   transcription factor PKDM7D
Arabidopsis thaliana AT4G20400   probable lysine-specific demethylase JMJ14
Arabidopsis thaliana AT2G34880   protein MATERNAL EFFECT EMBRYO ARREST 27
Babesia bovis BBOV_IV000510   jmjC transcription factor, putative
Brugia malayi Bm1_31510   jmjC domain containing protein
Candida albicans CaO19.13096   similar to S. cerevisiae YJR119C
Candida albicans CaO19.5651   similar to S. cerevisiae YJR119C
Caenorhabditis elegans CELE_ZK593.4   Protein RBR-2
Dictyostelium discoideum DDB_G0268778   ARID/BRIGHT DNA binding domain-containing protein
Drosophila melanogaster Dmel_CG9088   little imaginal discs
Echinococcus granulosus EgrG_001034900   Jumonji AT rich interactive domain 1B
Echinococcus granulosus EgrG_000332200   lysine specific demethylase 5A
Echinococcus multilocularis EmuJ_000332200   lysine specific demethylase 5A
Echinococcus multilocularis EmuJ_001034900   Jumonji, AT rich interactive domain 1B
Homo sapiens ENSG00000280358   lysine (K)-specific demethylase 5D
Homo sapiens ENSG00000126012   lysine (K)-specific demethylase 5C
Homo sapiens ENSG00000073614   lysine (K)-specific demethylase 5A
Homo sapiens ENSG00000117139   lysine (K)-specific demethylase 5B
Loa Loa (eye worm) LOAG_01817   jmjC domain-containing protein
Mus musculus ENSMUSG00000025332   lysine (K)-specific demethylase 5C
Mus musculus 75605   lysine (K)-specific demethylase 5B
Mus musculus ENSMUSG00000030180   lysine (K)-specific demethylase 5A
Mus musculus 20592   lysine (K)-specific demethylase 5D
Neospora caninum NCLIV_053150   hypothetical protein
Oryza sativa 4338043   Os05g0196500
Oryza sativa 4338351   Os05g0302300
Saccharomyces cerevisiae YJR119C   Jhd2p
Schistosoma japonicum Sjp_0110980   IPR011011,Zinc finger, FYVE/PHD-type,domain-containing
Schistosoma japonicum Sjp_0309440   expressed protein
Schistosoma japonicum Sjp_0011400   Histone demethylase rbr-2, putative
Schistosoma mansoni Smp_156290   jumonji/arid domain-containing protein
Schistosoma mansoni Smp_019170   jumonji/arid domain-containing protein
Schmidtea mediterranea mk4.001332.01   Lysine-specific demethylase lid
Schmidtea mediterranea mk4.009248.02  
Schmidtea mediterranea mk4.009248.00   Lysine-specific demethylase lid
Schmidtea mediterranea mk4.009248.01   Lysine-specific demethylase rbr-2
Schmidtea mediterranea mk4.016945.00  
Toxoplasma gondii TGME49_307010   histone lysine demethylase JMJC1/KDM5D/JARID1D
Toxoplasma gondii TGME49_205630   hypothetical protein

Essentiality

Sjp_0011400 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
CELE_ZK593.4 Caenorhabditis elegans embryonic lethal wormbase
TGME49_205630 Toxoplasma gondii Essentiality uncertain sidik
TGME49_307010 Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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

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
Species Known druggable target Linked compounds Reference
Homo sapiens lysine (K)-specific demethylase 5B Compounds References
Homo sapiens lysine (K)-specific demethylase 5C Compounds References
Mus musculus lysine (K)-specific demethylase 5A Compounds References
Homo sapiens lysine (K)-specific demethylase 5A Compounds References
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 Sjp_0011400 (Schistosoma japonicum), Histone demethylase rbr-2, putative
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