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 |
17 Allele
| Public Name |
|---|
| gk963801 |
| gk963053 |
| gk962682 |
| gk963357 |
| gk963356 |
| WBVar01244399 |
| gk154055 |
| WBVar01943555 |
| gk154054 |
| gk154053 |
| WBVar00175533 |
| WBVar00175534 |
| WBVar00175535 |
| gk376374 |
| gk836903 |
| gk681471 |
| gk896633 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00219205 | 10942216 | 10943417 | 1 |
11 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 | |
| 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 | |
| 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 | |
| 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). |