Genomics
2 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:Y27F2A.11b.1 | Y27F2A.11b.1 |
933
 |
II: 3189338-3190954 |
| Transcript:Y27F2A.11a.1 | Y27F2A.11a.1 |
984
|
II: 3189338-3190954 |
Other
2 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:Y27F2A.11b | Y27F2A.11b |
933
|
II: 3189338-3189493 |
| CDS:Y27F2A.11a | Y27F2A.11a |
984
|
II: 3189338-3189670 |
46 Allele
| Public Name |
|---|
| gk964317 |
| gk963801 |
| WBVar02122302 |
| WBVar02122780 |
| WBVar02124390 |
| WBVar02122098 |
| WBVar02122355 |
| gk962754 |
| WBVar02124872 |
| WBVar02121545 |
| WBVar02120617 |
| WBVar00091066 |
| WBVar02122218 |
| WBVar02121721 |
| WBVar02120928 |
| WBVar01695220 |
| tm11324 |
| WBVar01916129 |
| otn4888 |
| WBVar01235341 |
| WBVar02087265 |
| WBVar01536951 |
| WBVar01536950 |
| WBVar01536949 |
| WBVar01536948 |
| WBVar01536947 |
| WBVar00168713 |
| WBVar00168714 |
| WBVar00168712 |
| gk899367 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00045304 | 3189338 | 3190954 | 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_chrII_3190955..3191212 | 258 | II: 3190955-3191212 | Caenorhabditis elegans |
13 Expression Clusters
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| adult vs dauer larva | Transcripts that showed differential expression in adult vs dauer lava in N2 animals at 20C. | N.A. | WBPaper00050488:adult_vs_dauer_regulated_N2_20C |
| Genes up regulated by Tryptophan. | Differentially expressed genes had a fold change cutoff of 2.0 and an unpaired t test p value cutoff of 0.05 for WT+Trp versus WT and 0.01 for nhr-114 versus glp-1. | WBPaper00042194:Tryptophan_upregulated | |
| 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 | |
| Bacteria infection: Xenorhabdus nematophila | Caenorhabditis elegans Genes with expression levels changed significantly after treatment of Xenorhabdus nematophila. | Differential expression were calculated by empirical eBayes method using eBayes function. P_value <= 0.01 and log2 fold change > 1 were used to call differentially expressed genes in all datasets. | WBPaper00041606:CE_X.nematophila_regulated |
| UVC-EtBr-exposed(exposed to 7.5 J/m2 UVC radiation 3 times, 24 h apart (48 h total) and exposed to EtBr (5ug/mL in agar).) vs UVC-exposed(exposed to 7.5 J/m2 UVC radiation 3 times, 24 h apart (48 h total).) at just prior to the second UVC dose (24h). | Genes differentially expressed under EtBr treatment and UVC exposure vs under UVC exposure but without EtBr treatment at the -25h timepoint (just prior to the second UVC dose (24h)). | Transcripts were defined as fold-change >1.2, p < 0.05 based on Rosetta Resolver analysis for all pairwise treatment comparisons. The fold-change refers to the second intensity over the first. | WBPaper00041939:UVC-EtBr-exposed_vs_UVC-exposed_24h |
| Transcripts that showed significantly decreased expression glp-1(e2141); TU3401 animals comparing to in TU3401 animals. | Fold change > 2, FDR < 0.01. | WBPaper00065993:glp-1(e2141)_downregulated | |
| Down-regulated genes (fold change > 1.5) in two CoQ-deficient clk-1 mutant strains (e2519, qm30) compared to wild types N2. | Fold-changes of intensities were calculated from the arithmetic mean of gene expression values between experimental and corresponding control group. Fold change >= 1.5 was used as cut-off. | WBPaper00045774:clk-1_downregulated | |
| moderate static magnetic field | Transcripts that showed significantly decreased expression after exposure to moderate static magnetic field. | N.A. | WBPaper00064509:static-magnetic-field_downregulated |
| Bacteria Diet: L. plantarum with pdxH mutant vs. L. plantarum | Transcripts that showed significantly decreased expression in N2 animals fed with L. plantarum with pdxH mutant, comparing to in N2 animals fed with L. plantarum. | GFold3, logFC < -1 or > 1. | WBPaper00066703:L.plantarum-pdxH_downregulated |
| Transcripts that showed significantly decreased expression in daf-2(e1370) comparing to in N2. | Student's t-test, fold change > 2, p-value < 0.05. | WBPaper00055386:daf-2(e1370)_downregulated | |
| Genes that showed significantly increased expression after exposure to adsorbable organic bromine compounds (AOBr) contained in M. aeruginosa batch culture. | Differentially expressed genes (DEGs) were identified with a random variance t-test and a significance analysis of microarrays (SAM) test. Genes were considered statistically significant if their p-value was less than 0.05, the false discovery rate less than 0.3, and the fold change compared to control at least <= 0.67 or >=1.5. | WBPaper00046853:AOBr_M.aeruginosa-batch-culture_upregulated | |
| Transcripts that showed significantly decreased expression in swsn-1(os22ts) comparing to in N2 animals at young adult worms. | DESeq2, FDR<0.05 and fold-change 2. (Threshold set by WormBase curator.) | WBPaper00060764:swsn-1(os22ts)_downregulated | |
| C-lineage related expression profile. | QT clustering | WBPaper00025032:cluster_126 |
4 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr2025421 | 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). | |||
| Expr1159285 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| Expr2007189 | 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). | |||
| Expr1018353 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 |
1 Upstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrII_3188829..3189337 | 509 | II: 3188829-3189337 | Caenorhabditis elegans |
