Genomics
1 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:F55G7.5.1 | F55G7.5.1 |
518
 |
X: 11938130-11938926 |
Other
1 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:F55G7.5 | F55G7.5 |
435
|
X: 11938187-11938463 |
20 Allele
| Public Name |
|---|
| gk964260 |
| gk964029 |
| gk962707 |
| gk964028 |
| gk963810 |
| WBVar01571124 |
| WBVar01571123 |
| WBVar01690658 |
| gk661602 |
| WBVar01832060 |
| gk771685 |
| gk567145 |
| gk359403 |
| gk843708 |
| gk672249 |
| WBVar01571126 |
| WBVar01571125 |
| WBVar02009193 |
| WBVar00083380 |
| gk295263 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00195215 | 11938130 | 11938926 | -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_chrX_11935156..11938129 | 2974 | X: 11935156-11938129 | Caenorhabditis elegans |
8 Expression Clusters
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| 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 significantly decreased expression in eat-2(ad1116) comparing to in N2 at 3-days post L4 adult hermaphrodite animals. | DESeq2(v1.14.1), fold change > 2, p-value < 0.05 | WBPaper00055354:eat-2(ad1116)_downregulated | |
| Transcripts that showed significantly increased expression in dpy-21(e428) comparing to in N2 during L3 stage. | DESeq v1.6.3. Fold change > 1.5. | WBPaper00050370:dpy-21(e428)_L3_upregulated | |
| Transcripts that showed significantly decreased expression after animals were treated with 100uM Rapamycin and 50uM Rifampicin from day 1 to day 3 adult hermaphradite. | DESeq2(v1.14.1), fold change > 2, p-value < 0.05 | WBPaper00055354:Rapamycin-Rifampicin_downregulated | |
| Transcripts enriched in male him-5(e1490 animals, comparing to in N2 hermaphrodite animals from L3 larva to young adult stages. | DESeq FDR < 0.01. | WBPaper00050231:male_enriched | |
| Transcripts that interact with both BAZ-2 and SET-6 in Chip-Seq analysis. | N.A. | WBPaper00059356:BAZ-2_SET-6_interacting | |
| Top 300 transcripts enriched in AVL 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:AVL | |
| Transcripts interacting with LAG-1 at L4 larva stage in whole animal ChIP-Seq analysis. | edgeR fold change >= 2, FDR <= 0.05. | WBPaper00059440:LAG-1_interacting_WholeAnimal |
3 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr1152345 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| Expr2004251 | 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). | |||
| Expr2022473 | 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_chrX_11938927..11940335 | 1409 | X: 11938927-11940335 | Caenorhabditis elegans |
