Genomics
1 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:Y56A3A.41.1 | Y56A3A.41.1 |
638
 |
III: 11892171-11893039 |
Other
1 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:Y56A3A.41 | Y56A3A.41 |
570
|
III: 11892172-11892508 |
27 Allele
| Public Name |
|---|
| gk963887 |
| gk963147 |
| gk964363 |
| gk964364 |
| gk963799 |
| gk187124 |
| gk187125 |
| gk187126 |
| gk187127 |
| WBVar01771425 |
| WBVar01771426 |
| WBVar01771423 |
| WBVar01771424 |
| gk540749 |
| gk312875 |
| gk625994 |
| WBVar00217682 |
| WBVar00217681 |
| WBVar00217680 |
| WBVar00217679 |
| gk958297 |
| WBVar01579180 |
| WBVar01852548 |
| WBVar01508107 |
| WBVar01508108 |
| WBVar02030768 |
| WBVar01952997 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00269438 | 11892171 | 11893039 | -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_chrIII_11891436..11892170 | 735 | III: 11891436-11892170 | Caenorhabditis elegans |
13 Expression Clusters
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| Transcripts of coding genes that showed significantly decreased expression in muscle. | DESeq2 (version 1.24.0). Transcripts with a false-discovery rate adjusted p-value less than 0.05 were considered significantly differentially expressed. | WBPaper00062325:muscle_depleted_coding-RNA | |
| Transcripts that showed significantly increased expression in hda-1(ne4752[3xFLAG-Degron-HDA-1]) in gonads dissected from 1-day old adult animals. | Salmon was used to map the mRNA-seq reads with the worm database WS268, and its output files were imported to DESeq2 in R. The differentially expressed genes were filtered by fold change more than 2 and adjusted p-value < 0.05. The scatter plots were generated by the plot function in R. | WBPaper00061479:hda-1(ne4752)_upregulated | |
| Transcripts that showed significantly increased expression in mut-16(pk710), comparing to in N2 animals. | DESeq2 v. 1.22.2, adjusted p-value <= 0.05. | WBPaper00059605:mut-16(pk710)_upregulated | |
| Transcripts that showed significantly increased expression in ilc-17.1(syb5296) comparing to in N2 animals at L4 larva stage. | DESeq2, fold change > 2, FDR < 0.05. | WBPaper00066594:ilc-17.1(syb5296)_upregulated | |
| Transcripts that showed significantly decreased expression in let-767(RNAi) L4 animals comparing to animals fed with empty vector. | log2 fold change > 1.5 or < -1.5, p-value < 0.05 | WBPaper00066679:let-767(RNAi)_downregulated | |
| Temperature Shift: 25C vs 15C for 16 hours at L4 larva stage. | Transcripts that showed significantly increased expression in AFD neurons comparing to in whole animals. | DESeq2, fold change > 2, FDR < 0.05. | WBPaper00065158:AFD_enriched |
| Transcripts that showed significantly decreased expression in ogt-1(ok1474) neuronal cells isolated by FACs comparing to in FACs isolated neuronal cells from wild type. | DESeq2, fold change > 2, FDR < 0.05. | WBPaper00066485:ogt-1(ok1474)_downregulated_neuron | |
| Transcripts that showed significantly increased expression 2 hours after auxin-induced MOG-7-degron to remove endogenous MOG-7 protein. | N.A. | WBPaper00062146:MOG-7-degron_2h_regulated | |
| Transcripts that showed significantly increased expression in hrde-1(tm1200) in gonads dissected from 1-day old adult animals. | Salmon was used to map the mRNA-seq reads with the worm database WS268, and its output files were imported to DESeq2 in R. The differentially expressed genes were filtered by fold change more than 2 and adjusted p-value < 0.05. The scatter plots were generated by the plot function in R. | WBPaper00061479:hrde-1(tm1200)_upregulated | |
| Single-cell RNA-Seq cell group 28_0 expressed in neuron. | scVI 0.6.0 | WBPaper00065841:28_0 | |
| Transcripts that showed significantly increased expression in hrde-2(tm1200) comparing to in N2. | Fold change > 2, FDR < 0.05. | WBPaper00066448:hrde-2(tm1200)_upregulated | |
| Single-cell RNA-Seq cell group 86_0 expressed in neuron. | scVI 0.6.0 | WBPaper00065841:86_0 | |
| Single-cell RNA-Seq cell group 51_0 expressed in neuron. | scVI 0.6.0 | WBPaper00065841:51_0 |
2 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr2026248 | 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). | |||
| Expr2008007 | 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_chrIII_11893040..11894792 | 1753 | III: 11893040-11894792 | Caenorhabditis elegans |
