Genomics
1 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:H05L14.3.1 | H05L14.3.1 |
2052
 |
I: 7980231-7984758 |
Other
1 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:H05L14.3 | H05L14.3 |
1638
|
I: 7980237-7980305 |
49 Allele
| Public Name |
|---|
| gk962858 |
| gk962706 |
| gk963902 |
| gk963849 |
| gk964316 |
| gk962622 |
| tm10574 |
| gk963550 |
| WBVar00537796 |
| gk116035 |
| gk116036 |
| h15373 |
| h17369 |
| h14862 |
| WBVar01849684 |
| WBVar00154789 |
| WBVar00154790 |
| WBVar00154788 |
| WBVar00154793 |
| WBVar00154791 |
| WBVar00154792 |
| WBVar01909909 |
| WBVar01574016 |
| gk940019 |
| WBVar01957292 |
| gk482796 |
| gk411143 |
| gk764378 |
| gk702331 |
| gk429556 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00271605 | 7980231 | 7984758 | 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_chrI_7984759..7984888 | 130 | I: 7984759-7984888 | Caenorhabditis elegans |
14 Expression Clusters
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| Transcripts that showed significantly increased 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_upregulated_neural | |
| 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 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 | |
| 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 hda-1(RNAi) embryos comparing to control animals. | DESeq2, fold change > 2, FDR < 0.05. | WBPaper00067044:hda-1(RNAi)_upregulated | |
| Transcripts that showed significantly increased expression in sftb-1(cer6) deletion homozygous comparing to to in N2 animals at L4 larva stage. | DESeq2, fold change > 2 | WBPaper00058725:sftb-1(cer6)_upregulated | |
| Transcripts that showed significantly increased expression in lin-53(RNAi) embryos comparing to control animals. | DESeq2, fold change > 2, FDR < 0.05. | WBPaper00067044:lin-53(RNAi)_upregulated | |
| Transcripts that showed significantly increased expression in spr-5(by101) L1 animals comparing to in N2 control. | DeSeq2 (v.2.11.40.2), p < 0.05. | WBPaper00060886:spr-5(by101)_upregulated | |
| Top 300 transcripts enriched in AVG 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:AVG | |
| Single-cell RNA-Seq cell group 31_0 expressed in gonad. | scVI 0.6.0 | WBPaper00065841:31_0 | |
| Single-cell RNA-Seq cell group 57_0 expressed in epithelium. | scVI 0.6.0 | WBPaper00065841:57_0 | |
| Top 300 transcripts enriched in Z1, Z4 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:Z1_Z4 | |
| Single-cell RNA-Seq cell group 77_0 expressed in neuron. | scVI 0.6.0 | WBPaper00065841:77_0 |
2 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr2022752 | 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). | |||
| Expr2004526 | 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_chrI_7977079..7980230 | 3152 | I: 7977079-7980230 | Caenorhabditis elegans |
