Detailed view for PF3D7_1367100

Basic information

TDR Targets ID: 258
Plasmodium falciparum, U1 small nuclear ribonucleoprotein, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 9.8266 | Length (AA): 423 | MW (Da): 51835 | 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)
PF12220   U1 small nuclear ribonucleoprotein of 70kDa MW N terminal

Gene Ontology

Mouse over links to read term descriptions.
GO:0030619   U1 snRNA binding  
GO:0005685   snRNP U1  
GO:0003723   RNA binding  
GO:0003676   nucleic acid binding  
GO:0000166   nucleotide 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
65 207 1n52 (B) 7 150 20.00 0.000000025 0.94 0.61 0.09
78 185 1x4b (A) 6 115 22.00 0 1 0.44 0.07
91 209 2f9d (A) 12 124 19.00 0 0.73 0.44 -0.45
96 239 2cjk (A) 157 299 18.00 0.0000000000016 0.9 0.55 0.24
99 172 1no8 (A) 106 179 23.00 0.00000000003 1 0.66 -1.74
372 420 2kmk (A) 24 72 8.00 0.000000098 0.01 0.276539 -1.12
373 405 2em6 (A) 8 40 3.00 0.00061 0 0.326714 -2.51
34 177 3pgw (S) 38 183 47.00 0 1 0.837033 0.48
100 146 2dh8 (A) 12 59 32.00 0.31 1 0.569496 -0.69
382 414 2em6 (A) 8 40 3.00 0.00084 0 0.314389 -2.51
386 419 2eps (A) 412 446 12.00 0.02 0 0.272704 -1.37

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 Oocyst, Ring, Sporozoite, Female Gametocyte, Male Gametocyte. Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, gametocyte, sporozoite, early ring, early schizont, early trophozoite, late ring, late schizont. Otto TD PlasmoDB
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 24 hs, intra-erythrocytic - 40 hs, merozoite, late trophozoite. Otto TD PlasmoDB
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intra-erythrocytic - 32 hs, intra-erythrocytic - 48 hs. Otto TD
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
  • Lasonder E Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes. Molecular insight into sex-specific processes and translational repression.
  • 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.

Orthologs

Ortholog group members (OG5_128070)

Species Accession Gene Product
Arabidopsis thaliana AT3G50670   U1 small nuclear ribonucleoprotein-70K
Babesia bovis BBOV_II005790   u1 snRNP, putative
Brugia malayi Bm1_26575   RNA binding protein
Candida albicans CaO19.6866   similar to U1snRNP 70kd
Candida albicans CaO19.14156   similar to U1snRNP 70kd
Caenorhabditis elegans CELE_K04G7.10   Protein RNP-7
Cryptosporidium hominis Chro.60129   U1 small nuclear ribonucleoprotein
Cryptosporidium parvum cgd6_990   U1 snrp Snp1p. RRM domain containing protein
Dictyostelium discoideum DDB_G0268004   U1 small nuclear ribonucleoprotein 70 kDa protein
Drosophila melanogaster Dmel_CG8749   small ribonucleoprotein particle U1 subunit 70K
Echinococcus granulosus EgrG_001019100   RNA recognition motif RNP 1
Entamoeba histolytica EHI_153670   U1 small nuclear ribonucleoprotein subunit, putative
Echinococcus multilocularis EmuJ_001019100   RNA recognition motif, RNP 1
Homo sapiens ENSG00000104852   small nuclear ribonucleoprotein 70kDa (U1)
Leishmania braziliensis LbrM.16.1650   U1 small nuclear ribonucleoprotein, putative
Leishmania donovani LdBPK_161690.1   u1 small nuclear ribonucleoprotein 70 kDa
Leishmania infantum LinJ.16.1690   U1 small nuclear ribonucleoprotein, putative
Leishmania major LmjF.16.1590   U1 small nuclear ribonucleoprotein, putative
Leishmania mexicana LmxM.16.1590   U1 small nuclear ribonucleoprotein, putative
Loa Loa (eye worm) LOAG_10208   hypothetical protein
Mus musculus ENSMUSG00000063511   small nuclear ribonucleoprotein 70 (U1)
Neospora caninum NCLIV_020480   hypothetical protein
Oryza sativa 4347985   Os10g0115600
Plasmodium berghei PBANKA_1143000   U1 small nuclear ribonucleoprotein, putative
Plasmodium falciparum PF3D7_1367100   U1 small nuclear ribonucleoprotein, putative
Plasmodium knowlesi PKNH_1104100   U1 small nuclear ribonucleoprotein, putative
Plasmodium vivax PVX_115315   U1 small nuclear ribonucleoprotein 70 kDa, putative
Plasmodium yoelii PY00080   u1 small nuclear ribonucleoprotein 70 kDa
Saccharomyces cerevisiae YIL061C   Snp1p
Schistosoma japonicum Sjp_0212780   similar to U1 small nuclear ribonucleoprotein 70 kDa, putative
Schistosoma japonicum Sjp_0128520   similar to U1 small nuclear ribonucleoprotein 70 kDa, putative
Schistosoma japonicum Sjp_0069350   similar to U1 small nuclear ribonucleoprotein 70 kDa, putative
Schistosoma mansoni Smp_013360   U1 small nuclear ribonucleoprotein 70 kD
Schmidtea mediterranea mk4.002786.01   U1 small nuclear ribonucleoprotein 70 kDa
Trypanosoma brucei gambiense Tbg972.8.4640   U1 small nuclear ribonucleoprotein, putative
Trypanosoma brucei Tb927.8.4830   u1 small nuclear ribonucleoprotein 70 kDa
Trypanosoma congolense TcIL3000_8_4530   u1 small nuclear ribonucleoprotein 70 kDa
Trypanosoma cruzi TcCLB.508837.140   u1 small nuclear ribonucleoprotein 70 kDa
Trypanosoma cruzi TcCLB.511383.30   u1 small nuclear ribonucleoprotein 70 kDa
Toxoplasma gondii TGME49_205180   RNA recognition motif-containing protein
Theileria parva TP02_0544   U1 small nuclear ribonucleoprotein, putative
Trichomonas vaginalis TVAG_371310   U1 small nuclear ribonucleoprotein 70 kD, putative

Essentiality

PF3D7_1367100 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.8.4830 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.8.4830 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.8.4830 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.8.4830 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_K04G7.10 Caenorhabditis elegans embryonic arrest wormbase
CELE_K04G7.10 Caenorhabditis elegans embryonic lethal wormbase
CELE_K04G7.10 Caenorhabditis elegans larval arrest wormbase
CELE_K04G7.10 Caenorhabditis elegans slow growth wormbase
CELE_K04G7.10 Caenorhabditis elegans sterile wormbase
YIL061C Saccharomyces cerevisiae inviable yeastgenome
PBANKA_1143000 Plasmodium berghei Essential plasmo
TGME49_205180 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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
  • 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.
  • 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.
  • 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
  • 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
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930

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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Gene identifier PF3D7_1367100 (Plasmodium falciparum), U1 small nuclear ribonucleoprotein, putative
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