Genomics
1 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:F39E9.27.1 | F39E9.27.1 |
843
 |
II: 3299757-3300698 |
Other
1 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:F39E9.27 | F39E9.27 |
753
|
II: 3299825-3300148 |
49 Allele
| Public Name |
|---|
| gk964317 |
| gk963801 |
| gk963053 |
| WBVar02122302 |
| WBVar02120456 |
| WBVar02123019 |
| WBVar02122780 |
| WBVar02122532 |
| WBVar02124390 |
| WBVar02122098 |
| WBVar02122355 |
| WBVar02124673 |
| WBVar02124872 |
| WBVar02120786 |
| WBVar02120617 |
| WBVar02121131 |
| WBVar02123186 |
| WBVar02123659 |
| WBVar02121370 |
| WBVar02122914 |
| WBVar02122218 |
| WBVar02121721 |
| gk964209 |
| gk964210 |
| WBVar02124763 |
| WBVar02121950 |
| WBVar02120928 |
| tm10837 |
| WBVar02121546 |
| gk138080 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00269387 | 3299757 | 3300698 | 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_chrII_3300699..3302760 | 2062 | II: 3300699-3302760 | Caenorhabditis elegans |
8 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 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)_upregulated_neuron | |
| control(maintained under normal lab light (mostly dark, in incubators).) vs UVC-EtBr-exposed(exposed to 7.5 J/m2 UVC radiation 3 times, 24 h apart (48 h total) and exposed to EtBr (5ug/mL in agar).) at just prior to the third UVC dose (48h). | Genes differentially expressed in control vs after UVC exposure and EtBr treatment at the -1h timepoint (just prior to the third UVC dose (48h)). | Transcripts were defined as fold-change >1.2, p < 0.05 based on Rosetta Resolver analysis for all pairwise treatment comparisons. The fold-change refers to the second intensity over the first. | WBPaper00041939:control_vs_UVC-EtBr-exposed_48h |
| Transcripts that showed significantly decreased expression in unc-70(cas983) comparing to in N2 at L1 larva stage. | DESeq2, fold change >= 2, FDR <= 0.05 | WBPaper00057041:unc-70(cas983)_downregulated | |
| Transcripts that showed more than 4 fold of expression in N2 comparing to in CB4856 animals. | DESeq2, fold change > 4. | WBPaper00053909:N2_vs_CB4856_upregulated | |
| moderate static magnetic field | Transcripts that showed significantly increased expression after exposure to moderate static magnetic field. | N.A. | WBPaper00064509:static-magnetic-field_upregulated |
| Transcripts that showed significantly decreased expression in spc-1(cas971) comparing to in N2 at L1 larva stage. | DESeq2, fold change >= 2, FDR <= 0.05 | WBPaper00057041:spc-1(cas971)_downregulated | |
| Genes that showed decreased expression after 50uM DBAA treatment comparing with control. | Differentially expressed genes (DEGs) were identified with a random variance t test and a significance analysis of microarrays (SAM) test. Genes 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. | WBPaper00045294:50uM_DBAA_downregulated |
2 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr2009670 | 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). | |||
| Expr2027909 | 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_chrII_3299591..3299756 | 166 | II: 3299591-3299756 | Caenorhabditis elegans |
