WormMine

WSWS298

An integrated data resource for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00304815 Gene Name  Y40A1A.6
Sequence Name  ? Y40A1A.6 Organism  Caenorhabditis elegans
Automated Description  Enriched in coelomocyte; germ line; and neurons based on single-cell RNA-seq studies. Is affected by unc-30 and mir-238 based on RNA-seq studies. Is affected by cyclobutrifluram based on RNA-seq studies. Biotype  SO:0001263
Genetic Position  X:± Length (nt)  ? 177
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00304815

Genomics

1 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:Y40A1A.6 Y40A1A.6 177   X: 1998860-1999036
 

Other

0 CDSs

1 RNAi Result

WormBase ID
WBRNAi00059387

12 Allele

Public Name
gk963725
gk963864
WBVar01979570
WBVar02120741
WBVar02121915
WBVar02120540
WBVar02123551
WBVar01619170
gk730460
gk880643
gk819693
gk819692

1 Chromosome

WormBase ID Organism Length (nt)
X Caenorhabditis elegans 17718942  

1 Chromosome Location


Feature . Primary Identifier 		Start End Strand
WBGene00304815 1998860 1999036 -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_chrX_1998035..1998859   825 X: 1998035-1998859 Caenorhabditis elegans

24 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
  Transcripts that showed significantly decreased expression in N2 day 3 adults comparing to in N2 day 1 adult animals according to Oxford Nanopore Technologies Direct RNA sequencing (Nanopore DRS). DESeq fold change > 2, FDR < 0.05. WBPaper00067499:Day3_vs_Day1_downregulated_Nanopore
  Transcripts that showed significantly decreased expression in N2 day 4 adults comparing to in N2 day 1 adult animals according to Illumina RNASeq. DESeq fold change > 2, FDR < 0.05. WBPaper00067499:Day4_vs_Day1_downregulated_Illumina
  Transcripts that showed significantly decreased expression in N2 day 4 adults comparing to in N2 day 1 adult animals according to Oxford Nanopore Technologies Direct RNA sequencing (Nanopore DRS). DESeq fold change > 2, FDR < 0.05. WBPaper00067499:Day4_vs_Day1_downregulated_Nanopore
  Transcripts that showed significantly decreased expression in N2 day 5 adults comparing to in N2 day 1 adult animals according to Illumina RNASeq. DESeq fold change > 2, FDR < 0.05. WBPaper00067499:Day5_vs_Day1_downregulated_Illumina
  Transcripts that showed significantly decreased expression in N2 day 5 adults comparing to in N2 day 1 adult animals according to Oxford Nanopore Technologies Direct RNA sequencing (Nanopore DRS). DESeq fold change > 2, FDR < 0.05. WBPaper00067499:Day5_vs_Day1_downregulated_Nanopore
  Transcripts that showed significantly decreased expression in N2 day 7 adults comparing to in N2 day 1 adult animals according to Illumina RNASeq. DESeq fold change > 2, FDR < 0.05. WBPaper00067499:Day7_vs_Day1_downregulated_Illumina
  Transcripts that showed significantly decreased expression in N2 day 7 adults comparing to in N2 day 1 adult animals according to Oxford Nanopore Technologies Direct RNA sequencing (Nanopore DRS). DESeq fold change > 2, FDR < 0.05. WBPaper00067499:Day7_vs_Day1_downregulated_Nanopore
  Transcripts that showed significantly decreased expression in N2 day 10 adults comparing to in N2 day 1 adult animals according to Illumina RNASeq. DESeq fold change > 2, FDR < 0.05. WBPaper00067499:Day10_vs_Day1_downregulated_Illumina
  Transcripts that showed significantly decreased expression in N2 day 10 adults comparing to in N2 day 1 adult animals according to Oxford Nanopore Technologies Direct RNA sequencing (Nanopore DRS). DESeq fold change > 2, FDR < 0.05. WBPaper00067499:Day10_vs_Day1_downregulated_Nanopore
  Transcripts that showed significantly decreased expression in N2 day 15 adults comparing to in N2 day 1 adult animals according to Illumina RNASeq. DESeq fold change > 2, FDR < 0.05. WBPaper00067499:Day15_vs_Day1_downregulated_Illumina
  Transcripts that showed significantly decreased expression in N2 day 15 adults comparing to in N2 day 1 adult animals according to Oxford Nanopore Technologies Direct RNA sequencing (Nanopore DRS). DESeq fold change > 2, FDR < 0.05. WBPaper00067499:Day15_vs_Day1_downregulated_Nanopore
  Transcripts that showed significantly increased expression in npp-14(ax4543) comparing to in N2. DESeq2. Statistically significant genes were chosen based on a BenjaminiHochberg adjusted P-value of 0.05. WBPaper00067885:npp-14(ax4543)_upregulated
  Transcripts that showed significantly decreased expression in fic-1(n5823);hsp-4(RNAi) comparing to fic-1(n5823) animals with control vector. edgeR (v3.19, Bioconductor), p < 0.05, log2FC > 1.5 or < -1.5 WBPaper00068266:hsp-4(RNAi)_downregulated_fic-1(n5823)
  Transcripts enriched in Coelomocyte according to single cell RNAseq. Genes that pass the Bonferroni threshold for multiple comparisons (q < 0.05) are significantly enriched. WBPaper00061651:Coelomocyte_enriched
  Transcripts that showed significantly increased expression in unc-30(ok613) animals at L4 larva stage, comparing to N2 animals. Genes exhibiting at least two-fold change were considered differentially expressed. WBPaper00061439:unc-30(ok613)_upregulated
  Transcripts that showed significantly decreased expression in skn-1(lax188);daf-2(e1370) comparing to in daf-2(e1370) animals DESeq2, fold change > 2, FDR < 0.05. WBPaper00067765:skn-1(lax188)_downregulated_daf-2(e1370)
Bacteria infection: Staphylococcus epidermidis Transcripts that showed significantly decreased expression in mab-5(e1239) animals exposed to S. epidermidis for 24 hours since L4 larva stage, comparing to uninfected mab-5(e1239) animals. DESeq2, (FDR)-adjusted P-value < 0.05 and fold change >= 2. WBPaper00066587:S.epidermidis_downregulated_mab-5(e1239)
  Transcripts that showed significantly decreased expression in sma-3(wk30) comparing to in N2. EdgeR fold change > 2, FDR < 0.05. WBPaper00067781:sma-3(wk30)_downregulated
  Transcripts that showed significantly decrreased expression after 24 hours of exposure to nematicide cyclobutrifluram. DESeq2, fold change > 2, FDR <= 0.001. WBPaper00066118:cyclobutrifluram_downregulated
  Transcripts enriched in Germline according to single cell RNAseq. Genes that pass the Bonferroni threshold for multiple comparisons (q < 0.05) are significantly enriched. WBPaper00061651:Germline_enriched
  Transcripts enriched in SIA according to single cell RNAseq. Genes that pass the Bonferroni threshold for multiple comparisons (q < 0.05) are significantly enriched. WBPaper00061651:SIA_enriched
  Transcripts enriched in I4 according to single cell RNAseq. Genes that pass the Bonferroni threshold for multiple comparisons (q < 0.05) are significantly enriched. WBPaper00061651:I4_enriched
  Transcripts enriched in PHA according to single cell RNAseq. Genes that pass the Bonferroni threshold for multiple comparisons (q < 0.05) are significantly enriched. WBPaper00061651:PHA_enriched
  Transcripts that showed significantly decreased expression in miR-238(n4112) comparing to in N2 day 5 adults. DESeq2, fold change > 2, padj < 0.05 and baseMean >100 WBPaper00066207:mir-238(n4112)_downregulated

0 Expression Patterns

0 GO Annotation

0 Homologues

1 Locations


Feature . Primary Identifier 		Start End Strand
WBGene00304815 1998860 1999036 -1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

Length
177

1 Sequence Ontology Term

Identifier Name Description
gene  

0 Strains

1 Upstream Intergenic Region

WormBase ID Name Sequence Name Length (nt) Chromosome Location Organism
intergenic_region_chrX_1999037..2001029   1993 X: 1999037-2001029 Caenorhabditis elegans