WormMine

WS297

Intermine data mining platform for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00196202 Gene Name  W04D2.8
Sequence Name  ? W04D2.8 Organism  Caenorhabditis elegans
Automated Description  Is affected by several genes including ilc-17.1; chd-3; and let-418 based on RNA-seq and microarray studies. Is affected by multi-walled carbon nanotube based on RNA-seq studies. Biotype  SO:0001263
Genetic Position  Length (nt)  ? 129
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00196202

Genomics

1 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:W04D2.8 W04D2.8 129   V: 12475799-12475927
 

Other

0 CDSs

0 RNAi Result

8 Allele

Public Name
gk963271
gk963301
gk964458
gk964459
gk963618
gk557862
gk249631
gk249632

1 Chromosome

WormBase ID Organism Length (nt)
V Caenorhabditis elegans 20924180  

1 Chromosome Location


Feature . Primary Identifier
Start End Strand
WBGene00196202 12475799 12475927 -1

2 Data Sets

Name URL
WormBaseAcedbConverter  
C. elegans genomic annotations (GFF3 Gene)  

1 Downstream Intergenic Region

WormBase ID Name Sequence Name Length (nt) Chromosome Location Organism
intergenic_region_chrV_12474650..12475798   1149 V: 12474650-12475798 Caenorhabditis elegans

5 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
  Transcripts that showed significantly increased expression in ilc-17.1(syb5296) comparing to in N2 animals at L4 larva stage. DESeq2, fold change > 2, FDR < 0.05. WBPaper00066594:ilc-17.1(syb5296)_upregulated
Bacteria Diet: L. plantarum with pdxH mutant vs. L. plantarum Transcripts that showed significantly decreased expression in N2 animals fed with L. plantarum with pdxH mutant, comparing to in N2 animals fed with L. plantarum. GFold3, logFC < -1 or > 1. WBPaper00066703:L.plantarum-pdxH_downregulated
  Genes that showed significantly decreased expression after exposure to 1mg/L MWCNTs from L1 larva to young adult. Transcripts with false discovery rate-corrected p-values < 0.05 and fold change > 2 were defined as differentially expressed. WBPaper00049377:MWCNT_downregulated
  Transcripts that showed significantly decreased expression in eat-2(ad465) comparing to in N2. Student's t-test, fold change > 2, p-value < 0.05. WBPaper00055386:eat-2(ad465)_downregulated
  Transcripts that showed significantly increased expression in 24-cell stage embryo of chd-3(eh4)let-418(RNAi) animals, comparing to in N2 animals injected with gfp control RNAi vector. DESeq and EdgeR were used. A threshold of 1.5 log2 fold change and a p value <10 % were applied. let-418: wild-type; let-418(RNAi)-treated embryos; chd-3: chd-3(eh4);controlGFP(RNAi)-treated embryos; chd-3_let-418: chd-3(eh4); let-418(RNAi)-treated embryos. All fold changes are calculated versus wild-type;control(RNAi)-treated embryos. 1h and 3h correspond to the 24- and 100-cell stages, respectively. WBPaper00050163:chd-3(eh4);let-418(RNAi)_upregulated_100-cell-embryo

0 Expression Patterns

0 GO Annotation

0 Homologues

1 Locations


Feature . Primary Identifier
Start End Strand
WBGene00196202 12475799 12475927 -1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

Length
129

1 Sequence Ontology Term