WormMine

WSWS298

An integrated data resource for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00219205 Gene Name  R03D7.15
Sequence Name  ? R03D7.15 Organism  Caenorhabditis elegans
Automated Description  Enriched in GLR and neurons based on RNA-seq and single-cell RNA-seq studies. Is affected by bcat-1 and skn-1 based on RNA-seq studies. Biotype  SO:0001217
Genetic Position  :± Length (nt)  ? 1202
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00219205

Genomics

1 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:R03D7.15.1 R03D7.15.1 605   II: 10942216-10943417
 

Other

1 CDSs

WormMine ID Sequence Name Length (nt) Chromosome Location
CDS:R03D7.15 R03D7.15 225   II: 10942532-10942672

1 RNAi Result

WormBase ID
WBRNAi00075539

17 Allele

Public Name
gk963801
gk963053
gk962682
gk963357
gk963356
WBVar01244399
gk154055
WBVar01943555
gk154054
gk154053
WBVar00175533
WBVar00175534
WBVar00175535
gk376374
gk836903
gk681471
gk896633

1 Chromosome

WormBase ID Organism Length (nt)
II Caenorhabditis elegans 15279421  

1 Chromosome Location


Feature . Primary Identifier 		Start End Strand
WBGene00219205 10942216 10943417 1

2 Data Sets

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

0 Downstream Intergenic Region

15 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
  Neuronally enriched transcripts according to a comparison of neuronal nuclei IP samples to total nuclei using isolation of nuclei from tagged specific cell types (INTACT) technology. DESEQ2, fold change > 2 and FDR < 0.01. WBPaper00062103:neuron_enriched
  Transcipts that showed significantly decreased expression in old (days 24, 14, and 9 of adulthood) octr-1(ok371) comparing to in N2 at 25C. DESeq2 v1.31.16, fold change > 2, FDR < 0.05 WBPaper00068082:octr-1(ok371)_downregulated_old_25C
  Transcripts that showed significantly changed expression in 6-day post-L4 adult hermaphrodite comparing to in 1-day post L4 adult hermaphrodite animals. Sleuth WBPaper00051558:aging_regulated
  Transcripts that showed significantly increased expression in the F2 (second generation) of ulp-2(tv380) gonad comparing to in N2 gonad. DESeq2, p < 0.05 WBPaper00067685:ulp-2(tv380)_upregulated_F2-gonad
Temprature shift to 28C for 24 hours. Transcripts that showed significantly increased expression after animals were exposed to 28C temperature for 24 hours. Differentially expressed genes wereidentified using DESeq (v.1.18.0) by normalizing readsbased on the negative binomial distribution method andcomparing each HS timepoint to the 0-h control. WBPaper00061341:28C_24h_upregulated
Temprature shift to 28C for 48 hours. Transcripts that showed significantly increased expression after animals were exposed to 28C temperature for 48 hours. Differentially expressed genes wereidentified using DESeq (v.1.18.0) by normalizing readsbased on the negative binomial distribution method andcomparing each HS timepoint to the 0-h control. WBPaper00061341:28C_48h_upregulated
  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
  Transcripts that showed significantly increased expression in the neurons of bcat-1(RNAi) animals at 5-days post L4 adult hermaphrodite stage, comparing to animals injected with empty vector. DESeq2. FDR < 0.05. WBPaper00060459:bcat-1(RNAi)_upregulated
  Transcripts that showed significantly increased expression in skn-1gf(lax188) comparing to in N2 animals at L4 stage fed with OP50 and exposed to PA14 for 4 hours. DESeq2, FDR < 0.05, fold change > 2. WBPaper00067255:skn-1(lax188)_upregulated_PA
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
  Single-cell RNA-Seq cell group 145_0 expressed in neuron. scVI 0.6.0 WBPaper00065841:145_0
  Single-cell RNA-Seq cell group 23_0 expressed in mesoderm. scVI 0.6.0 WBPaper00065841:23_0
  Single-cell RNA-Seq cell group 19_0 expressed in neuron. scVI 0.6.0 WBPaper00065841:19_0
  Single-cell RNA-Seq cell group 112_0 expressed in neuron. scVI 0.6.0 WBPaper00065841:112_0
Wounded by glass wool. Proteins that showed significantly decreased expression 24 hours after wounded by glass wool. Fold change > 2 or < 0.5. WBPaper00061285:wounding_24h_downregulated

3 Expression Patterns

Remark Reporter Gene Primary Identifier Pattern Subcellular Localization
    Expr2023564 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).  
    Expr1154878 Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015  
    Expr2005344 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
WBGene00219205 10942216 10943417 1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

Length
1202

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_chrII_10942199..10942215   17 II: 10942199-10942215 Caenorhabditis elegans