Genomics
9 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:T09E8.1h.1 | T09E8.1h.1 |
3183
 |
V: 13152919-13175996 |
| Transcript:T09E8.1i.1 | T09E8.1i.1 |
795
|
V: 13152920-13154024 |
| Transcript:T09E8.1g.1 | T09E8.1g.1 |
3174
|
V: 13153941-13176111 |
| Transcript:T09E8.1c.1 | T09E8.1c.1 |
2769
|
V: 13155323-13175583 |
| Transcript:T09E8.1f.1 | T09E8.1f.1 |
2076
|
V: 13156784-13175583 |
| Transcript:T09E8.1b.1 | T09E8.1b.1 |
2070
|
V: 13159728-13175583 |
| Transcript:T09E8.1a.1 | T09E8.1a.1 |
3129
|
V: 13161401-13176115 |
| Transcript:T09E8.1e.1 | T09E8.1e.1 |
1644
|
V: 13167416-13175583 |
| Transcript:T09E8.1d.1 | T09E8.1d.1 |
1649
|
V: 13172794-13175583 |
Other
9 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:T09E8.1h | T09E8.1h |
2769
|
V: 13152920-13153087 |
| CDS:T09E8.1c | T09E8.1c |
2769
|
V: 13155323-13155595 |
| CDS:T09E8.1f | T09E8.1f |
2076
|
V: 13156784-13156841 |
| CDS:T09E8.1b | T09E8.1b |
2070
|
V: 13159728-13159779 |
| CDS:T09E8.1a | T09E8.1a |
2244
|
V: 13161754-13161979 |
| CDS:T09E8.1d | T09E8.1d |
1644
|
V: 13172799-13173041 |
| CDS:T09E8.1e | T09E8.1e |
1644
|
V: 13167416-13167570 |
| CDS:T09E8.1g | T09E8.1g |
1788
|
V: 13164170-13164468 |
| CDS:T09E8.1i | T09E8.1i |
795
|
V: 13152920-13153087 |
445 Allele
| Public Name |
|---|
| gk963271 |
| gk963706 |
| gk963301 |
| gk964458 |
| gk964459 |
| WBVar02061720 |
| WBVar02061721 |
| WBVar02061722 |
| WBVar02061723 |
| WBVar02061704 |
| WBVar02061705 |
| WBVar02061706 |
| WBVar02061707 |
| WBVar02061708 |
| WBVar02061709 |
| WBVar02061710 |
| WBVar02061711 |
| WBVar02061712 |
| WBVar02061713 |
| WBVar02061714 |
| WBVar02061715 |
| WBVar02061716 |
| WBVar02061717 |
| WBVar02061718 |
| WBVar02061719 |
| otn10203 |
| otn10204 |
| otn10205 |
| gk964462 |
| WBVar01869029 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00011647 | 13152919 | 13176115 | 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_13176116..13176710 | 595 | V: 13176116-13176710 | Caenorhabditis elegans |
209 Expression Clusters
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| Genes with expression altered >= 3-fold in dpy-10(e128) mutants. | Data across the wild type series was analyzed using the Significance analysis of Microarrays (SAM) algorithm (to calculate the False Discovery Rate (FDR)). | WBPaper00035873:dpy-10_regulated | |
| Transcripts expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons. | DESeq. False discovry rate (FDR) < 0.1. | WBPaper00048988:neuron_expressed | |
| 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 |
| Transcripts that showed significantly higher expression in somatic gonad precursor cells (SGP) vs. head mesodermal cells (hmc). | DESeq2, fold change >= 2, FDR <= 0.01. | WBPaper00056826:SGP_biased | |
| Starvation 48 hours at L1 arrest | Transcripts that showed significantly increased expression in starved N2 animals (48 hours at L1 arrest) | Fold change > 2. | WBPaper00064005:starvation_upregulated_N2_mRNA |
| Transcripts expressed in the epithelial tissues surrounding the pharynx that includes the arcade and intestinal valve (AIV) cells, according to PAT-Seq analysis using Pbath-15-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:arcade_intestinal-valve_expressed | |
| Transcripts expressed in body muscle, according to PAT-Seq analysis using Pmyo-3-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:body-muscle_expressed | |
| Transcripts expressed in GABAergic neuron, according to PAT-Seq analysis using Punc-47-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:GABAergic-neuron_expressed | |
| Proteins interacting with NHR-49-GFP according to co-IP and LC-MS. | N.A. | WBPaper00064071:NHR-49_interacting | |
| Transcripts that showed altered expression in cat-1(RNAi) animals comparing to control animals injected with empty vector. | p-value <= 0.05 | WBPaper00066902:cat-1(RNAi)_regulated | |
| Transcripts expressed in hypodermis, according to PAT-Seq analysis using Pdpy-7-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:hypodermis_expressed | |
| Transcripts expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:intestine_expressed | |
| Strictly maternal class (SM): genes that are the subset of maternal genes that are not also classified as embryonic. | A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing. | [cgc5767]:expression_class_SM | |
| Transcripts expressed in NMDA neuron, according to PAT-Seq analysis using Pnmr-1-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:NMDA-neuron_expressed | |
| Transcripts expressed in pharynx, according to PAT-Seq analysis using Pmyo-2-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:pharynx_expressed | |
| Genes with expression level regulated by genotype (N2 vs CB4856) and age at old adults stage (214 hours at 24 centigrade). | For model 2, authors used 100 permutations to estimate the FDR threshold. Per permutation, genotypes and ages were independently randomly distributed, keeping the among-gene structure intact. Then for each spot (23,232) on the array, model 2 was tested. The obtained P-values were used to estimate a threshold for each of the explanatory factors. Authors also used a genome-wide threshold of -log10 P-value = 2, which resembles an FDR of 0.072 and 0.060 for marker and the interaction age-marker for the developing worms and FDR of 0.050 and 0.065 for marker and age-marker for the aging worms. For the physiological age effect, authors used a log10 P-value = 8 in developing worms (0.012 FDR) and -log10 P-value = 6 (0.032 FDR). | WBPaper00040858:eQTL_age_regulated_aging | |
| Transcripts expressed in seam cells, according to PAT-Seq analysis using Pgrd-10-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:seam_expressed | |
| Genes with expression level regulated by genotype (N2 vs CB4856) at old adults stage (214 hours at 24 centigrade). | For model 2, authors used 100 permutations to estimate the FDR threshold. Per permutation, genotypes and ages were independently randomly distributed, keeping the among-gene structure intact. Then for each spot (23,232) on the array, model 2 was tested. The obtained P-values were used to estimate a threshold for each of the explanatory factors. Authors also used a genome-wide threshold of -log10 P-value = 2, which resembles an FDR of 0.072 and 0.060 for marker and the interaction age-marker for the developing worms and FDR of 0.050 and 0.065 for marker and age-marker for the aging worms. For the physiological age effect, authors used a log10 P-value = 8 in developing worms (0.012 FDR) and -log10 P-value = 6 (0.032 FDR). | WBPaper00040858:eQTL_regulated_aging | |
| Genes with expression level regulated by genotype (N2 vs CB4856) at Late reproduction stage (96 hours at 24 centigrade). | Authors permuted transcript values and used a genome-wide threshold of log10 P-value = 2, which resembles a false discovery rate (FDR) of 0.0118. | WBPaper00040858:eQTL_regulated_reproductive | |
| Bacteria infection: Photorhabdus luminescens | Genes down-regulated in animals infected with Photorhabdus luminescens compared to the E. coli OP50 control after 24h of infection. | MAANOVA and BRB-Array-Tools. | WBPaper00030985:Photorhabdus_luminescens_downregulated |
| Bacteria infection: Bacillus thuringiensis | mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 2 mix) vs BT407 12h), according to RNAseq. | Cuffdiff, ajusted p-value < 0.01. | WBPaper00046497:B.thuringiensis_0.5mix_downregulated_12h |
| Transcripts detected in germline isolated from day-1 adult hermaphrodite animals. | All three experiments have CPM >= 1. | WBPaper00067147:germline_expressed | |
| Transcripts that showed significantly decreased expression in hsp-6(mg585) comparing to in N2 at L4 larva stage. | EdgeR, fold change > 2, FDR < 0.001. | WBPaper00056290:hsp-6(mg585)_downregulated | |
| starvation 12 hours | Transcripts that showed significantly increased expression in dissected intestines of N2 L1 larva that were starved for 12 hours, comparing to fed animals. | EdgeR, FDR < 0.05, fold change >= 2. | WBPaper00067259:starvation_upregulated_intestine |
| Bacteria infection: Staphylococcus aureus MW2. 4 hours of exposure. | Transcripts that showed significantly increased expression after N2 animals had 4 hours of infection by Staphylococcus aureus (MW2). | DEseq 1.18.0, adjusted p-value < 0.05. | WBPaper00056471:S.aureus-4h_upregulated_N2 |
| Transcripts that showed significantly increased expression in animals exposed to 400uM tamoxifen from L1 to L4 larva stage. | DEseq2, fold change > 2 | WBPaper00064505:tamoxifen_upregulated | |
| Transcripts that showed significantly changed expression in 6-day post-L4 adult hermaphrodite comparing to in 1-day post L4 adult hermaphrodite animals. | Sleuth | WBPaper00051558:aging_regulated | |
| Significantly differentially expressed genes as determined by microarray analysis of wild-type and cde-1 mutant germlines. | RNAs that changed at least 2-fold with a probability of p < 0.05 were considered differentially regulated between wildtype and cde-1. | WBPaper00035269:cde-1_regulated | |
| Transcripts that showed significantly altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage. | DESeq | WBPaper00053302:stavudine_24h_regulated | |
| Genes down regulated by mir-243(n4759). | RNAs that changed at least 2-fold with a probability of p > 0.05 in three biological replicates were considered differentially regulated between wild-type and mir-243. | WBPaper00036130:mir-243_down_regulated |
12 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr14754 | We found that both PTRN-1 and NOCA-1 localize to the apical ncMTOC in wild-type embryonic intestinal cells. | |||
| Expr12458 | Imaging of a GFP fusion with NOCA-1 in the larval epidermis revealed that it had a localization pattern very similar to that of γ-tubulin; NOCA-1 and γ-tubulin were both observed in puncta in the epidermal syncytium where the microtubule bundles are present and also concentrated along the junctions between the epidermal body syncytium and the seam cells. In the germline, NOCA-1 and γ-tubulin co-localize at the cell surface. NOCA-1 do not co-localize with γ-tubulin at centrosomes. In double label images of NOCA-1d::GFP or PTRN- 1::GFP with tagRFP::β-tubulin many puncta of both proteins were observed coincident with the microtubule bundles in the body epidermis. | |||
| Expr1021374 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
| Expr1153566 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| Expr1035131 | Tiling arrays expression graphs | |||
| Expr1034601 | Tiling arrays expression graphs | |||
| Expr1012639 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
| Expr12608 | NOCA-1 concentrated at hemidesmosomes and seam-seam adherens junctions. | |||
| Expr2043090 | Translational efficiency and RNA abundance/Ribosome occupancy across early embryonic stages (1-cell to 8-cell). For each developmental stage, translational efficiency was calculated as the ratio between ribosome footprint reads and mRNA abundance after normalization. A detailed description of the experimental methods and analysis can be found in: Shukla Y, Ghatpande V, Hu CF, Dickinson DJ, Cenik C. Landscape and regulation of mRNA translation in the early C. elegans embryo. Cell Rep. 2025 June 24;44(6):115778. doi: 10.1016/j.celrep.2025.115778. PMID: 40450690 | |||
| Expr2014346 | 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). | |||
| Expr2032587 | 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). | |||
| Expr1156565 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 |
14 GO Annotation
| Annotation Extension | Qualifier |
|---|---|
| enables | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| occurs_in(WBbt:0007846) | involved_in |
| involved_in | |
| involved_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in |
14 Ontology Annotations
| Annotation Extension | Qualifier |
|---|---|
| enables | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| occurs_in(WBbt:0007846) | involved_in |
| involved_in | |
| involved_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in |
1 Upstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrV_13152467..13152918 | 452 | V: 13152467-13152918 | Caenorhabditis elegans |
