Genomics
1 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:Y70C5A.4.1 | Y70C5A.4.1 |
264
 |
V: 16617762-16618080 |
Other
1 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:Y70C5A.4 | Y70C5A.4 |
264
|
V: 16617762-16617847 |
25 Allele
| Public Name |
|---|
| gk963271 |
| WBVar02123303 |
| WBVar02124908 |
| gk964050 |
| WBVar02123708 |
| WBVar02124497 |
| WBVar02124626 |
| WBVar02124059 |
| WBVar02121634 |
| gk963302 |
| WBVar02124267 |
| WBVar02122684 |
| WBVar02121793 |
| WBVar02123140 |
| WBVar02124428 |
| WBVar02124831 |
| WBVar02122859 |
| WBVar01907495 |
| WBVar02079619 |
| gk858866 |
| WBVar00040045 |
| WBVar01634375 |
| WBVar01593813 |
| WBVar01778476 |
| WBVar01778477 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00194799 | 16617762 | 16618080 | 1 |
3 Data Sets
| Name | URL |
|---|---|
| WormBaseAcedbConverter | |
| GO Annotation data set | |
| C. elegans genomic annotations (GFF3 Gene) |
1 Downstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrV_16618081..16618337 | 257 | V: 16618081-16618337 | Caenorhabditis elegans |
5 Expression Clusters
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| Transcripts expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:intestine_expressed | |
| Transcripts unqiuely expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:intestine_enriched | |
| Transcripts that showed significantly increased exression in animals exposed to 100uM cadmium for 24 hours. | DESeq2 v1.20.0, fold change > 2, FDR < 0.05. | WBPaper00065029:cadmium_upregulated | |
| Top 300 transcripts enriched in ABplapppapp, ABprapppapp according to single cell RNAseq. | Top 300 enriched transcripts were determined by log2.ratio of the tpm in the cell type vs the tpm in the other cells * the log2 of the cell.type tpm. | WBPaper00061340:Neuroblast_HSN_PHB | |
| mRNAs that showed increased expression after 100ug\/L microcystin-LR exposure. | Differentially expressed genes (DEGs) were identified with a random-variance t-test and an SAM (Significance Analysis of Microarrays) test. Gene expression differences were considered statistically significant if their p-value was less than 0.05, the false discovery rate less than 0.3 and the fold-change compared to control at least <= 0.67 or >= 1.5. | WBPaper00045807:microcystin-LR_upregulated |
3 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr2008263 | 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). | |||
| Expr1161534 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| Expr2026505 | 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). |
1 Upstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrV_16615129..16617761 | 2633 | V: 16615129-16617761 | Caenorhabditis elegans |
