Genomics
1 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:C06A12.19.1 | C06A12.19.1 |
441
 |
IV: 17439610-17440101 |
Other
1 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:C06A12.19 | C06A12.19 |
258
|
IV: 17439643-17439833 |
23 Allele
| Public Name |
|---|
| gk964500 |
| gk962765 |
| gk963888 |
| gk962761 |
| gk962759 |
| gk963492 |
| gk963300 |
| WBVar01970355 |
| WBVar01543091 |
| WBVar01822055 |
| WBVar02070129 |
| gk960377 |
| gk379689 |
| gk473188 |
| gk778739 |
| WBVar01840875 |
| WBVar01673600 |
| WBVar01673598 |
| WBVar01673599 |
| WBVar01673597 |
| WBVar02098340 |
| WBVar02114486 |
| WBVar01583326 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00255702 | 17439610 | 17440101 | -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_chrIV_17439170..17439609 | 440 | IV: 17439170-17439609 | 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 csr-1a(tor159) comparing to in N2 at 25C. | DESeq2, fold change > 2, p-value < 0.05. | WBPaper00061753:csr-1(tor159)_upregulated_25C | |
| Transcripts expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:intestine_expressed | |
| Single-cell RNA-Seq cell group 45_0 expressed in glia. | scVI 0.6.0 | WBPaper00065841:45_0 | |
| Single-cell RNA-Seq cell group 141_0 expressed in glia. | scVI 0.6.0 | WBPaper00065841:141_0 | |
| Transcripts enriched in PHsh according to single cell RNAseq. | Genes that pass the Bonferroni threshold for multiple comparisons (q < 0.05) are significantly enriched. | WBPaper00061651:PHsh_enriched | |
| Transcripts that showed significantly increased expression in AGP22 [nhr-49(nr2041)I;glp-1(e2141)III] comparing to in CF1903 [glp-1(e2144)III] at Day 2 adults. | Fold change > 2, p Value of < 0.05 and a false discovery rate (FDR) of < 0.05. | WBPaper00061530:nhr-49(e2144)_upregulated | |
| Transcripts that showed significantly decreased expression in L1 neural cells comparing to in adult neural cells. | DESeq2 (v1.18.1) fold change > 2, P-adj<0.05, using BenjaminiHochberg correction. | WBPaper00060811:L1_vs_adult_downregulated_neural | |
| Transcripts that showed significantly increased expression in lpd-3(ok2138) comparing to in N2 animals. | DESeq2, fold change > 4, FDR < 0.05. | WBPaper00064661:lpd-3(ok2138)_upregulated | |
| Single-cell RNA-Seq cell group 30_5 expressed in glia. | scVI 0.6.0 | WBPaper00065841:30_5 | |
| Single-cell RNA-Seq cell group 79_0 expressed in glia. | scVI 0.6.0 | WBPaper00065841:79_0 | |
| Top 300 transcripts enriched in AIZL, AIZR 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:AIZ | |
| Single-cell RNA-Seq cell group 79_2 expressed in glia. | scVI 0.6.0 | WBPaper00065841:79_2 |
2 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr2000494 | 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). | |||
| Expr2018719 | 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_chrIV_17440102..17440606 | 505 | IV: 17440102-17440606 | Caenorhabditis elegans |
