Genomics
3 Transcripts
| Class | WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|---|
| MRNA | Transcript:C26D10.5b.1 | C26D10.5b.1 |
2249
 |
II: 8346684-8350563 |
| MRNA | Transcript:C26D10.5a.1 | C26D10.5a.1 |
2346
|
II: 8346690-8350559 |
| NcPrimaryTranscript | Transcript:C26D10.5c | C26D10.5c |
1925
|
II: 8346694-8350194 |
Other
2 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:C26D10.5b | C26D10.5b |
1791
|
II: 8346694-8346850 |
| CDS:C26D10.5a | C26D10.5a |
1977
|
II: 8346694-8346850 |
65 Allele
| Public Name |
|---|
| gk963801 |
| gk963053 |
| gk962682 |
| gk963446 |
| gk963257 |
| h9612 |
| WBVar01393874 |
| WBVar00173957 |
| ok1021 |
| hy21 |
| gk148714 |
| WBVar01538327 |
| WBVar00226214 |
| WBVar00226213 |
| WBVar01308536 |
| gk148720 |
| WBVar01308535 |
| gk148719 |
| zz7 |
| gk148722 |
| gk148721 |
| cas618 |
| gk148716 |
| gk148715 |
| gk148718 |
| gk148717 |
| ku433 |
| WBVar01242212 |
| ku434 |
| WBVar01242213 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00001159 | 8346684 | 8350563 | 1 |
3 Data Sets
| Name | URL |
|---|---|
| WormBaseAcedbConverter | |
| GO Annotation data set | |
| C. elegans genomic annotations (GFF3 Gene) |
195 Expression Clusters
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| Transcripts expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons. | DESeq. False discovry rate (FDR) < 0.1. | WBPaper00048988:neuron_expressed | |
| Transcripts that showed significantly increased expression glp-1(e2141); TU3401 animals comparing to in TU3401 animals. | Fold change > 2, FDR < 0.01. | WBPaper00065993:glp-1(e2141)_upregulated | |
| 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 | |
| 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 |
| Bacteria infection: Enterococcus faecalis | Genes with increased expression after 24 hours of infection by E.faecalis Fold changes shown are pathogen vs OP50. | For RNA-seq and tiling arrays, log2 fold changes between gene expression values of infected versus uninfected nematodes were calculated. For log2 fold changes > 0.00001 the values > 81.25th percentile were defined as up-regulated and for log2 fold changes < -0.00001 the values < 18.75th percentile were defined as down-regulated. | WBPaper00038438:E.faecalis_24hr_upregulated_TilingArray |
| Transcripts that showed significantly increased expression after animals were treated with 50uM Rifampicin from day 1 to day 3 adult hermaphradite. | DESeq2(v1.14.1), fold change > 2, p-value < 0.05 | WBPaper00055354:Rifampicin_upregulated | |
| Transcripts that showed significantly increased expression in eft-2(RNAi) animals at N2 background. | DESeq2, fold change > 2 and p-value < 0.01. | WBPaper00067953:eft-2(RNAi)_upregulated_N2 | |
| Transcripts that showed significantly increased expression in eif-2alpha(RNAi) animals at N2 background. | DESeq2, fold change > 2 and p-value < 0.01. | WBPaper00067953:eif-2alpha(RNAi)_upregulated_N2 | |
| Transcripts expressed in hypodermis, according to PAT-Seq analysis using Pdpy-7-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:hypodermis_expressed | |
| Transcripts that showed significantly decreased expression in atfs-1(cmh15) (null allele) animals comparing to in N2 animals at L4 larva stage. | edgeR, fold change > 2, FDR < 0.05 | WBPaper00060909:atfs-1(cmh15)_downregulated | |
| Transcripts expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:intestine_expressed | |
| Transcripts that showed significantly decreased expression at 5-days-post L4 adult N2 hermaphrodites comparing to 1-day-post L4 adult N2 hermaphrodites. | DESeq2, fold change > 2, FDR < 0.05 | WBPaper00065835:Day5_vs_Day1_downregulated | |
| Genes with expression level regulated by genotype (N2 vs CB4856) and age at L3 larva and Late reproduction stage (96 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_developing | |
| Transcripts that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals. | Fold change > 2, FDR < 0.05 | WBPaper00064088:Day-3-adult_vs_L4_downregulated_daf-16(mu86);glp-1(e2141) | |
| Transcripts that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals. | Fold change > 2, FDR < 0.05 | WBPaper00064088:Day-3-adult_vs_L4_downregulated_glp-1(e2141) | |
| Transcripts that showed significantly increased expression in rrf-3(pk1426) comparing to in N2 at embryo stage. | DESeq2v 1.18.1, fold change > 1.5, adjusted p-value < 0.01. | WBPaper00056169:rrf-3(pk1426)_upregulated_embryo | |
| Bacteria: Pseudomonas donghuensis HYS | Transcripts that showed significantly increased expression after 24 hours of infection by Pseudomonas donghuensis HYS with deletion of ferric uptake regulator (FUR), comparing to control animals exposed to OP50. | DESeq2, fold change > 2, FDR < 0.05. | WBPaper00068216:FUR_vs_OP50_upregulated |
| Bacteria infection: Bacillus thuringiensis | Transcripts that showed significantly increased 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_upregulated |
| Transcripts that showed significantly increased expression in sin-3(tm1276) comparing to in N2. | DESeq2, fold change > 2, p-value < 0.01. | WBPaper00061203:sin-3(tm1276)_upregulated | |
| Transcripts that showed significantly increased expression after four-day-old young adult worms were placed on NGM plates seeded with OP50 in the presence 5% Agaro-oligosaccharides(AGO) for 24 h, comparing to animals grown in the absence of AGO. | Fold change > 2. | WBPaper00064306:Agaro-oligosaccharides_upregulated | |
| Transcripts that showed significantly increased expression in exos-8(RNAi) animals. | fold change > 2, FDR < 0.05 | WBPaper00068292:exos-8(RNAi)_upregulated | |
| Transcripts that showed significantly increased expression in aak-1(tm1944);aak-2(ok524) animals comparing to in N2. | DEseq 1.18.0, adjusted p-value < 0.05. | WBPaper00056471:aak-1(tm1944);aak-2(ok524)_upregulated | |
| Transcripts that showed signifcantly increased expression in ubr-5(miy31) injected with empty vector comparing to in N2 animals injected with empty vector at L1 larva stage and collected at L4 larva stage. | FDR < 0.05, fold change > 2 | WBPaper00067368:ubr-5(miy31)_upregulated_N2 | |
| Transcripts that showed significantly altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage. | DESeq | WBPaper00053302:stavudine_24h_regulated | |
| Transcripts that showed significantly decreased expression in sin-3(tm1276) comparing to in N2 at early embryo when there were only 3 -5 eggs in the adult. | DESeq2, fold change > 2, adjusted p-value < 0.01 | WBPaper00058598:sin-3(tm1276)_downregulated | |
| Transcripts depleted in purified oocyte P bodies comparing to in the whole animal. | DESeq2, FDR < 0.05, fold change > 2. | WBPaper00065975:P-body_vs_WholeAnimal_depleted | |
| Transcripts that showed significantly decreased expression in dissected female germline comparing to in dissected male germline. | Log2 Fold change > 2 or <-1, p-value < 0.05. | WBPaper00053599:female_vs_male_downregulated | |
| Genes that showed expression levels higher than the corresponding reference sample (L2 all cell reference). | A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes. | WBPaper00037950:A-class-motor-neurons_L2-larva_expressed | |
| Genes that showed expression levels higher than the corresponding reference sample (L2 all cell reference). | A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes. | WBPaper00037950:all-neurons_L2-larva_expressed | |
| Genes that showed oscillating mRNA expression level throughout the 16 hour time courses from L3 larva to young adult. | The following three lines of R code were used to perform the classification: increasing <-2*amplitude-PC1 < -1.7; oscillating <-!increasing & (amplitude > 0.55); flat <-!increasing & !oscillating; Note that the amplitude of a sinusoidal wave corresponds to only half the fold change between trough and peak. | WBPaper00044736:oscillating_dev_expression |
17 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr1030737 | Tiling arrays expression graphs | |||
| Expr1837 | Expression of eff-1p::gfp was silent through the first third of embryogenesis, first appearing about 230 min after first cleavage in a subset of epidermal precursor cells. Over the next 3 hr, these and additional fluorescent cells were observed to migrate over the ventral and dorsal surfaces of the embryo, and the majority of GFP-positive cells fused to form the hyp6 and hyp7 syncytia. As elongation progressed, GFP was also expressed in a pair of cells that fused to form the binucleate "tail spike" . After hatching, eff-1p::gfp expression persisted in large epidermal syncytia through adulthood. Mononucleated epidermal cells-including the seam cells and the VPCs-remained nonfluorescent until shortly before undergoing larval fusion events. More specifically, GFP was seen in (1) nonstem daughters of the seam cells shortly before they fused into hyp7; (2) vulval cells invaginating to form toroids during morphogenesis; and (3) the rays and fan of the adult male tail. Expression was also seen in nonepidermal organs known to contain syncytia, including the pharynx and uterus. Interestingly, a few cells that express eff-1p::gfp have never been observed to fuse, such as some ventral epidermal precursors in the embryo and several neurons. | |||
| Expr7312 | Click the movie links below for interactive 4D movies of a fluorescence reporter. http://glowormnotes.blogspot.com/2009/10/eff-1gfp-trancriptional-fusion.html | |||
| Expr7304 | Click the movie links below for interactive 4D movies of a fluorescence reporter. http://glowormnotes.blogspot.com/2009/10/eff-1gfp-translational-fusion.html | |||
| Picture:Figure 6B. | Expr8129 | eff-1::EFF-1::GFP was expressed at high levels in vpi1 beginning at about 7 hr, but was never expressed in pm8. | ||
| Expr3230 | In the bean-stage preelongation embryo of a wild-type strain, EFF-1::GFP was initially seen in a punctate but unpolarized pattern in cells of the ventral and dorsal hypodermis. As expression increased, a uniform cytoplasmic fluorescence appeared surrounding the bright punctate bodies (possibly endoplasmic reticulum or Golgi apparatus). Isolated EFF-1::GFP-expressing cells, with no brightly expressing neighbors, retained an unpolarized distribution of fluorescence. In contrast, EFF-1::GFP became discretely and rapidly localized to contacts between pairs of brightly expressing fusion partner cells. Two types of EFF-1::GFP-enriched contacts could be observed: novel contacts between cells already expressing EFF-1::GFP and preexisting contacts between neighbors in which EFF-1::GFP expression arose after the contact was made. In the first case (novel contacts), two ventral cells expressing EFF-1::GFP migrated toward each other to meet at the ventral midline. Although fluorescence was not plasma-membrane associated during cell migration, a brightly fluorescent junction formed within minutes of initial contact between the two cells. This localization grew in intensity over the next 20 min. In the second case (preexisting contacts), two neighboring dorsal cells began to express EFF-1::GFP. At the interface between these cells, localized EFF-1::GFP became brighter in coincidence with their overall expression of EFF-1::GFP. In both cases (novel and preexisting contacts), the increase in localized fluorescence was approximately linear with time. Furthermore, the contact-localized fluorescence achieved intensities far exceeding the mere sum of brightness of two separate cell membranes, indicating continuous targeted accumulation at the interface. In dorsal hypodermal cells, EFF-1::GFP accumulated along the apical edge of the cell-cell interface, coincident with the intercellular junctions and the known origin of the fusion aperture between cells. Interestingly, the membrane accumulation of EFF-1::GFP persisted, even after the contents of two cells were mixed, indicating that cell fusion was underway or complete. In occasional recordings of ventral cells, the localized EFF-1::GFP appeared to be pushed aside, presumably by the widening cell-fusion aperture, as the cells fused. | |||
| Expr12734 | EFF-1 was first detected at the bean stage within individual puncta in the dorsal and ventral hypodermal cells before fusion. Subsequently, EFF-1 appeared as punctate staining in the cytoplasm of hyp6 and hyp7 precursor cells at the comma stage. Following embryonic fusions, EFF-1 remained vesicular, and the number of EFF-1 puncta increased when cell fusion was nearly completed. EFF-1 puncta showed minor co-localization with apical cell junctions detected by anti-DLG-1 antibody. EFF-1 puncta were aligned along longitudinal lines lying parallel to the seam cells. This arrangement might be dictated by the organization of the cytoskeleton in the syncytial hypodermal cells, where actin, intermediate filaments, and microtubules form bundles that run parallel to the seam cells. Thus, EFF-1 is expressed in puncta at the onset, during, and after hypodermal cell fusion in developing embryos. | |||
| Expr12735 | EFF-1 localization in C. elegans embryonic epidermal cells is tightly maintained in early endosomes by the RAB-5- and DYN-1-dependent endocytic machinery. The EFF-1 protein is dynamically delivered to all apical plasma membranes transiently and without specificity to the place of fusion. | |||
| Expr2011185 | 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). | |||
| Expr9648 | Peff-1::gfp was expressed at the L4 stage in VulA, VulC and less frequently in VulF. | |||
| Expr11944 | Analysis of wild-type worms showed that eff-1p::GFP was expressed in the daughter cells of P3.p, P4.p, and P8.p that are committed to fusion, and was absent in the daughter cells of P(5-7).p which escape the fusion fate. | |||
| Expr1145302 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| Expr1024244 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
| Expr15010 | EFF-1 was mainly localized to dynamic cytoplasmic vesicles but not with myr::mKate2 before wounding. | |||
| Expr14268 | In the uninjured, wild-type axon, EFF-1 formed an indiscriminate punctate pattern as we previously reported (Neumann et al., 2015). In the cell body, it was also present as intracellular puncta, with no clear localization to the cell membrane. | |||
| Expr13340 | After seam cell division in larvae, EFF-1::GFP was expressed in V.a but not in the non-fusing V.p. In contrast to observations in embryos, EFF-1::GFP was enriched at the fusion sites 155 ± 20 min (n = 21) after V.a formation, and gradually reached its highest intensities before fusion pore formation (i.e., the exchange of cellular content between two fusing cells; 3.3-fold increase of EFF-1::GFP fluorescence in V.a compared with V.p). Thus, EFF-1 was enriched at the fusion sites on the plasma membranes in larvae. | |||
| Expr2029421 | 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). |
29 GO Annotation
| Annotation Extension | Qualifier |
|---|---|
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| part_of | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| involved_in | |
| located_in | |
| involved_in | |
| involved_in | |
| enables | |
| enables | |
| enables | |
| enables |
29 Ontology Annotations
| Annotation Extension | Qualifier |
|---|---|
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| part_of | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| involved_in | |
| located_in | |
| involved_in | |
| involved_in | |
| enables | |
| enables | |
| enables | |
| enables |
1 Upstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrII_8338415..8346683 | 8269 | II: 8338415-8346683 | Caenorhabditis elegans |
