Genomics
1 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:F02D8.9.1 | F02D8.9.1 |
452
 |
V: 14954883-14955776 |
Other
1 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:F02D8.9 | F02D8.9 |
312
|
V: 14955021-14955230 |
17 Allele
| Public Name |
|---|
| gk963271 |
| gk963301 |
| gk964458 |
| gk964459 |
| gk963796 |
| gk963805 |
| WBVar02024688 |
| tm11289 |
| gk254772 |
| gk254773 |
| gk254774 |
| WBVar01775606 |
| gk578599 |
| gk473281 |
| gk614553 |
| WBVar02049986 |
| WBVar02054922 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00206370 | 14954883 | 14955776 | -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_14954734..14954882 | 149 | V: 14954734-14954882 | Caenorhabditis elegans |
12 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 | |
| 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 | |
| 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 | |
| Transcipts that showed significantly increased expression in old (days 24, 14, and 9 of adulthood) octr-1(ok371) comparing to in N2 at 25C. | DESeq2 v1.31.16, fold change > 2, FDR < 0.05 | WBPaper00068082:octr-1(ok371)_upregulated_old_25C | |
| Bacteria infection: Bacillus thuringiensis | Transcripts that showed significantly decreased expression in N2 animals infected by bacteria BMB171/Cry5Ba, an acrystalliferous Bt mutant BMB171 transformed with toxin gene cry5Ba on the shuttle vector pHT304, comparing to N2 animals infected by BMB171/pHT304. | N.A. | WBPaper00064229:B.thuringiensis-Cry5Ba_downregulated |
| Transcripts that showed significantly increased expression in sensory neuron (labeled by iaIs25[Pgcy-37::GFP + unc-119(+)]) comparing to in whole worm. | Fold change > 2, p-value < 0.05. | WBPaper00060661:sensory-neuron_enriched | |
| Transcripts that showed significantly increased expression in alh-4(hj221) deletion allele comparing to in N2. | N.A. | WBPaper00061653:alh-4(hj221)_upregulated | |
| Top 300 transcripts enriched in ASJL, ASJR 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:ASJ | |
| Transcripts that showed significantly decreased expression in met-2(n4256) L1 animals comparing to in N2 control. | DeSeq2 (v.2.11.40.2), p < 0.05. | WBPaper00060886:met-2(n4256)_downregulated | |
| Top 300 transcripts enriched in ASIL, ASIR 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:ASI | |
| Transcripts that showed significantly decreased expression in spr-5(by101);met-2(n4256) L1 animals comparing to in N2 control. | DeSeq2 (v.2.11.40.2), p < 0.05. | WBPaper00060886:spr-5(by101);met-2(n4256)_downregulated |
3 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr2020440 | 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). | |||
| Expr2002219 | 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). | |||
| Expr1147787 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 |
1 Upstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrV_14955777..14964513 | 8737 | V: 14955777-14964513 | Caenorhabditis elegans |
