Genomics
1 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:K12D9.11.1 | K12D9.11.1 |
518
 |
V: 3010926-3011494 |
Other
1 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:K12D9.11 | K12D9.11 |
225
|
V: 3010937-3011020 |
27 Allele
| Public Name |
|---|
| gk963301 |
| gk963591 |
| gk963553 |
| gk964259 |
| gk963850 |
| gk963027 |
| gk962689 |
| gk962688 |
| WBVar01586198 |
| WBVar01586199 |
| WBVar01972023 |
| gk964200 |
| WBVar02023359 |
| WBVar00205470 |
| gk229833 |
| gk229831 |
| gk229832 |
| gk593971 |
| gk540852 |
| gk474341 |
| gk897929 |
| WBVar01738998 |
| WBVar01738996 |
| WBVar01738997 |
| WBVar01614206 |
| WBVar01674178 |
| WBVar01738995 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00005882 | 3010926 | 3011494 | -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_3010569..3010925 | 357 | V: 3010569-3010925 | Caenorhabditis elegans |
8 Expression Clusters
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| Coexpression clique No. 203, sre-33-ZK1025.1_8337, on the genome-wide coexpression clique map for the nematode GPL200 platform. | All available microarray datasets for the GPL200 platform (Affymetrix C. elegans Genome Array) were obtained from the GEO repository. This included 2243 individual microarray experiments. These were normalized against each other with the software RMAexpress (Bolstad, 2014). Based on these normalized values, Pearsons correlation coefficients were obtained for each probe-probe pair of the 22,620 probes represented on this array type. The resulting list of correlation coefficients was then ranked to generate the ranked coexpression database with information on each probe represented on the GPL200 platform. | WBPaper00061527:sre-33-ZK1025.1_8337 | |
| Transcripts that showed significantly decreased expression in hpl-2(tm1489) comparing to in N2 animals. | DESeq2, adjusted p-value < 0.05, log2 fold change > 2 or < -2. | WBPaper00054493:hpl-2(tm1489)_downregulated | |
| Transcripts that showed significantly increased expression in animals lacking P granules by RNAi experiments targeting pgl-1, pgl-3, glh-1 and glh-4, and unc-119-GFP(-), comparing to in control animals, at 2-day post L4 adult hermaphrodite stage. | DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2. | WBPaper00050859:upregulated_P-granule(-)GFP(-)_vs_control_day2-adult | |
| Transcripts that showed significantly increased expression in cfp-1(tm6369) comparing to in N2 at early embryo stage. | DESeq2, FDR < 0.05 | WBPaper00058691:cfp-1(tm6369)_upregulated | |
| Transcripts that showed significantly increased expression in csr-1(RNAi) comparing to in N2 animals fed wth empty vector. | DESeq2 v1.20.0,, fold change > 2, FDR < 0.05. | WBPaper00066919:csr-1(RNAi)_upregulated | |
| Transcripts that showed significantly increased expression in set-2(bn129) comparing to in N2 at early embryo stage. | DESeq2, FDR < 0.05 | WBPaper00058691:set-2(bn129)_upregulated | |
| Top 300 transcripts enriched in I5 neuron 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:I5 | |
| Drug treatment: Elbe sediment | Genes with significantly changing transcripts in C. elegans exposed to the Elbe (E) sediment. | [ANOVA, p < 0.05 without multiple sample correction, fold-change to reference sediment Danube (D) > 1.4 (up-regulated) or < 0.7 (down-regulated)]. | WBPaper00033070:Elbe_downregulated |
2 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr2034932 | 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). | |||
| Expr2016754 | 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_3011495..3012694 | 1200 | V: 3011495-3012694 | Caenorhabditis elegans |
