Genomics
1 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:C02H6.3.1 | C02H6.3.1 |
936
 |
V: 7386675-7387855 |
Other
1 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:C02H6.3 | C02H6.3 |
936
|
V: 7386675-7387245 |
21 Allele
| Public Name |
|---|
| gk963301 |
| gk963553 |
| gk964259 |
| gk964351 |
| gk963850 |
| gk962860 |
| WBVar01862587 |
| gk964449 |
| gk239234 |
| gk239235 |
| gk239236 |
| snx3213 |
| WBVar01741188 |
| gk856514 |
| gk596824 |
| gk834548 |
| gk411773 |
| gk961725 |
| tm11526 |
| ttTi36972 |
| ttTi36985 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00220257 | 7386675 | 7387855 | -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_7386103..7386674 | 572 | V: 7386103-7386674 | Caenorhabditis elegans |
15 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 | |
| Neuronally enriched transcripts according to a comparison of neuronal nuclei IP samples to total nuclei using isolation of nuclei from tagged specific cell types (INTACT) technology. | DESEQ2, fold change > 2 and FDR < 0.01. | WBPaper00062103:neuron_enriched | |
| Transcripts that showed significantly increased expression in csr-1a(tor159) comparing to in N2 at 25C. | DESeq2, fold change > 2, p-value < 0.05. | WBPaper00061753:csr-1(tor159)_upregulated_25C | |
| Transcripts that showed significantly altered expression at URX, AQR, and PQR neurons in camt-1(ok515) animals comparing to in wild type AX1888-1 strain. | RNA-seq data were mapped using PRAGUI - a Python 3-based pipeline for RNA-seq data analysis. | WBPaper00061902:camt-1(ok515)_regulated_URX-AQR-PQR | |
| 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 increased expression in hda-2(ok1479) comparing to in N2 animals. | DESeq2 (version 1.28.1), FDR < 0.01, fold change > 2. | WBPaper00062159:hda-2(ok1479)_upregulated | |
| Transcripts that showed significantly decreased expression in mrps-5(RNAi) animals comparing to animals injected with empty vector. | Differential expression was assessed using a Partial least-squares discriminant analysis (PLS-DA) using mixomics setting a variable of importance (VIP) score of greater than 1 as significant. | WBPaper00059328:mrps-5(RNAi)_downregulated_mRNA | |
| Transcripts that showed significantly increased expression in FACS sorted neuron cells (labelled by pan-neuronal GFP) from edIs6[unc-119::GFP + rol-6(su1006)]; thoc-5(wy822) comparing to in edIs6. | DESeq2, log2 fold change > 2, adjusted p-value < 0.005. | WBPaper00055103:thoc-5(wy822)_upregulated | |
| Single-cell RNA-Seq cell group 11_2 expressed in epithelium. | scVI 0.6.0 | WBPaper00065841:11_2 | |
| Single-cell RNA-Seq cell group 81_0 expressed in neuron. | scVI 0.6.0 | WBPaper00065841:81_0 | |
| Single-cell RNA-Seq cell group 47_0 expressed in neuron. | scVI 0.6.0 | WBPaper00065841:47_0 | |
| Transcripts enriched in ADL according to single cell RNAseq. | Genes that pass the Bonferroni threshold for multiple comparisons (q < 0.05) are significantly enriched. | WBPaper00061651:ADL_enriched | |
| Single-cell RNA-Seq cell group 47_1 expressed in neuron. | scVI 0.6.0 | WBPaper00065841:47_1 | |
| Single-cell RNA-Seq cell group 99_0 expressed in neuron. | scVI 0.6.0 | WBPaper00065841:99_0 | |
| Transcripts enriched in PHA according to single cell RNAseq. | Genes that pass the Bonferroni threshold for multiple comparisons (q < 0.05) are significantly enriched. | WBPaper00061651:PHA_enriched |
2 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr2018569 | 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). | |||
| Expr2000345 | 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_7387856..7388389 | 534 | V: 7387856-7388389 | Caenorhabditis elegans |
