WormMine

WSWS298

An integrated data resource for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00235304 Gene Name  Y116A8C.468
Sequence Name  ? Y116A8C.468 Organism  Caenorhabditis elegans
Automated Description  Is affected by several genes including dve-1; atfs-1; and alh-4 based on RNA-seq studies. Is affected by four chemicals including antimycin; Doxycycline; and Tamoxifen based on RNA-seq studies. Biotype  SO:0001217
Genetic Position  :± Length (nt)  ? 123
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00235304

Genomics

1 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:Y116A8C.468.1 Y116A8C.468.1 123   IV: 16918379-16918501
 

Other

1 CDSs

WormMine ID Sequence Name Length (nt) Chromosome Location
CDS:Y116A8C.468 Y116A8C.468 123   IV: 16918379-16918501

2 RNAi Result

WormBase ID
WBRNAi00044748
WBRNAi00013385

9 Allele

Public Name
gk964078
gk964500
gk962765
gk963590
gk963795
gk962529
gk963948
gk963888
WBVar02122004

1 Chromosome

WormBase ID Organism Length (nt)
IV Caenorhabditis elegans 17493829  

1 Chromosome Location


Feature . Primary Identifier 		Start End Strand
WBGene00235304 16918379 16918501 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_chrIV_16918502..16919150   649 IV: 16918502-16919150 Caenorhabditis elegans

18 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
  Transcripts that showed significantly decreased expression in N2 animals exposed to 0.1mM Paraquat from hatching to reaching adult stage. DESeq2 version 1.22.2, p < 0.05 WBPaper00064716:paraquat_downregulated
  Transcripts that showed significantly decreased expression in dissected female germline comparing to in dissected male germline. Log2 Fold change > 2 or <-1, p-value < 0.05. WBPaper00053599:female_vs_male_downregulated
  Transcripts that showed altered expression from P0 to F2 generation animals after N2 parental generation were treated with antimycin, but not in damt-1(gk961032) P0 to F2 animals after the parenal generaton were treated with antimycin. N.A. WBPaper00055862:antimycin_damt-1(gk961032)_regulated
  Transcripts that showed significantly decreased expression in eat-2(ad465);dve-1(RNAi) animals comparing to eat-2(ad465) animals injected with empty vector. fold change > 2, FDR < 0.01 WBPaper00067391:dve-1(RNAi)_downregulated_eat-2(ad465)
  siRNAs that showed significantly lower expression (log2fold > 2, padj < 0.01) in hermaphrodite gonad (somatic gonad plus germine) than in male gonad (somatic gonad plus germine). DESeq2 v1.13.8, fold change > 2, FDR < 0.01. WBPaper00056161:male_enriched_siRNA
25C vs. 20C Transcripts that showed significantly decreased expression in 1-day post L4 adult hermaphrodite N2 grown at 25C, comparing to in N2 animals grown at 20C. CuffDiff, fold change > 2. WBPaper00065096:25C_vs_20C_downregulated
  Transcripts that showed significantly increased expression in mip-1(how5) comparing to in control animals. DESeq2, fold change > 2. WBPaper00066038:mip-1(how5)_upregulated
Bacteria diet: Escherichia coli HB101. Fed for 30 generations. Transcripts that showed significantly increased expression after fed by bacteria E. coli HB101 for 30 generations comparing to animals fed by E. coli OP50. DESeq2 fold change > 2, p-value < 0.01. WBPaper00061007:HB101_upregulated
  Transcripts that showed significantly decreased expression in eat-2(ad465);atfs-1(RNAi) animals comparing to eat-2(ad465) animals injected with empty vector. fold change > 2, FDR < 0.01 WBPaper00067391:atfs-1(RNAi)_downregulated_eat-2(ad465)
  Transcripts that showed significantly increased expression in skn-1(lax188);daf-2(e1370) comparing to in skn-1(lax188) animals DESeq2, fold change > 2, FDR < 0.05. WBPaper00067765:daf-2(e1370)_upregulated_skn-1(lax188)
  Transcripts that showed significantly increased expression in N2 comparing to in skn-1 gain of function allele lax188 animals DESeq2, fold change > 2, FDR < 0.05. WBPaper00067765:skn-1(lax188)_downregulated_N2
  Transcripts that showed significantly increased expression in N2 animals growing in 15mg per mL doxycycline from L1 to L4 larva stage. edgeR (version 3.24.3), fold change > 4, FDR < 0.01. WBPaper00062456:doxycycline_upregulated_N2_transcript
  Genes that were enriched in spermatogenic fem-3(q96gf) gonads comparing to in oogenic fog-2(q71), according to RNAseq analysis. To identify differentially expressed transcripts, authors used R/Bioconductor package DESeq. WBPaper00045521:Spermatogenic
  Transcripts that showed significantly decreased expression in animals exposed to 400uM tamoxifen from L1 to L4 larva stage. DEseq2, fold change > 2 WBPaper00064505:tamoxifen_downregulated
  Transcripts that showed significantly decreased expression in 10-days post L4 adult hermaphrodite N2 grown at 20C, comparing to in 1-day post L4 adult hermaphrodite N2 animals grown at 20C. CuffDiff, fold change > 2. WBPaper00065096:Day10_vs_Day1_downregulated
  Transcripts that showed significantly decreased expression in ceh-37(ok642) comparing to in N2 Fold change > 2, FDR < 0.05 WBPaper00067667:ceh-37(ok642)_downregulated
Starvation for 8 hours at mid-L4 larva stage. Transcripts that showed significantly decreased expression in cep-1(gk138) animals starved for 8 hours on unseeded plate at mid-L4 larva stage. Differential expression analysis was performed using the quasi-likelihood F-test with the generalized linear model (GLM) approach in edgeR. Fold change > 2, FDR < 0.05. WBPaper00067829:starvation_dowmregulated_cep-1(gk138)
  Transcripts that showed significantly decreased expression in alh-4(hj221) deletion allele comparing to in N2. N.A. WBPaper00061653:alh-4(hj221)_downregulated

1 Expression Patterns

Remark Reporter Gene Primary Identifier Pattern Subcellular Localization
    Expr2007057 Single cell embryonic expression. Only cell types with an expression fraction of greater 0.2 of the maximum expressed fraction are labeled (Full data can be downloaded from http://caltech.wormbase.org/pub/wormbase/datasets-published/packer2019/). The colors represent the broad cell class to which the cell type has been assigned. The size of the point is proportional to the log2 of the numbers of cells in the dataset of that cell type. Interactive visualizations are available as a web app (https://cello.shinyapps.io/celegans/) and can also be installed as an R package (https://github.com/qinzhu/VisCello.celegans).  

0 GO Annotation

0 Homologues

1 Locations


Feature . Primary Identifier 		Start End Strand
WBGene00235304 16918379 16918501 1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

Length
123

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_chrIV_16917932..16918378   447 IV: 16917932-16918378 Caenorhabditis elegans