Genomics
1 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:F25D1.8.1 | F25D1.8.1 |
153
 |
V: 10539414-10539925 |
Other
1 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:F25D1.8 | F25D1.8 |
153
|
V: 10539414-10539513 |
14 Allele
| Public Name |
|---|
| gk963301 |
| gk964451 |
| gk964452 |
| gk963495 |
| gk963496 |
| gk964351 |
| tm10541 |
| gk964304 |
| gk332694 |
| WBVar00001730 |
| gk802013 |
| WBVar02111885 |
| WBVar01864927 |
| WBVar01743155 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00195256 | 10539414 | 10539925 | 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_10539926..10540323 | 398 | V: 10539926-10540323 | Caenorhabditis elegans |
5 Expression Clusters
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| Transcripts with promoter regions binding DREAM protein complex, according to ChIP-seq of E2F-DP (DPL-1 and EFL-1) and MuvB (LIN-9, LIN-37, LIN-52, and LIN-54) of N2 late embryo. | N.A. | WBPaper00053289:DREAM-target | |
| 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 |
| Transcripts that interact with endogenous EGL-43-GFP at L3 larva stage according to CHIP-Seq analysis. | N.A. | WBPaper00059471:EGL-43_interacting | |
| Transcripts that showed significantly increased expression in alh-4(hj221) deletion allele comparing to in N2. | N.A. | WBPaper00061653:alh-4(hj221)_upregulated | |
| Top 300 transcripts enriched in rectal gland cell 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:Rectal_gland |
3 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr2021169 | 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). | |||
| Expr1149408 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| Expr2002953 | 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_10539126..10539413 | 288 | V: 10539126-10539413 | Caenorhabditis elegans |
