WormMine

WS294

Intermine data mining platform for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00090382 Gene Name  Ppa-smg-6
Sequence Name  ? PPA00828 Organism  Pristionchus pacificus
Automated Description  Predicted to enable DNA binding activity and catalytic activity. Predicted to be involved in base-excision repair. Is an ortholog of C. elegans smg-6. In C. elegans, smg-6 is involved in embryonic genitalia morphogenesis; nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; and regulatory ncRNA-mediated post-transcriptional gene silencing. Biotype  SO:0001217
Genetic Position  :±
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1 Organism

Name Taxon Id
Pristionchus pacificus 54126

0 Synonyms

Genomics

1 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:PPA00828.1 PPA00828.1   [unknown]
 

Other

1 CDSs

WormMine ID Sequence Name Length (nt) Chromosome Location
CDS:PPA00828 PPA00828   [unknown]

0 RNAi Result

0 Allele

0 Chromosome

0 Chromosome Location

2 Data Sets

Name URL
WormBaseAcedbConverter  
GO Annotation data set  

0 Downstream Intergenic Region

2 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
  Pristionchus pacificus genes up regulated in the dauer versus dauer-exit worms. The weight parameters were optimized based on MA-plots such that spike-in controls show their expected fold change values. lmFit function was used to fit a linear model to probe intensities across arrays, and differential expression was calculated by empirical Bayes method using the eBayes function. Control of FDR was employed as correction for multiple testing. WBPaper00041207:PP_dauer_up
Germline ablation Genes that showed differential expression in the comparision of germline-ablated animals fed on E. coli OP50 versus un-ablated animals fed E. coli OP50. Differential expression was calculated by empirical Bayes method using the eBayes function, and control of FDR was employed as the multiple testing correction. Authors used cutoff of absolute log2 fold change greater than or equal to 1.5 AND p_value less than or equal to 0.05 to call differentially expressed genes. WBPaper00041466:PP_germline-ablation_regulated

0 Expression Patterns

4 GO Annotation

Annotation Extension Qualifier
  enables
  involved_in
  involved_in
  enables

0 Homologues

0 Locations

4 Ontology Annotations

Annotation Extension Qualifier
  enables
  involved_in
  involved_in
  enables

0 Regulates Expr Cluster

0 Sequence

1 Sequence Ontology Term