Genomics
12 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:C10C5.1a.1 | C10C5.1a.1 |
7751
 |
IV: 9343359-9366510 |
| Transcript:C10C5.1b.1 | C10C5.1b.1 |
7638
|
IV: 9343359-9366511 |
| Transcript:C10C5.1f.1 | C10C5.1f.1 |
7636
|
IV: 9343362-9366506 |
| Transcript:C10C5.1d.1 | C10C5.1d.1 |
7640
|
IV: 9343362-9366510 |
| Transcript:C10C5.1j.1 | C10C5.1j.1 |
5567
|
IV: 9343363-9355568 |
| Transcript:C10C5.1l.1 | C10C5.1l.1 |
3117
|
IV: 9343737-9349140 |
| Transcript:C10C5.1i.1 | C10C5.1i.1 |
5115
|
IV: 9343737-9355568 |
| Transcript:C10C5.1k.1 | C10C5.1k.1 |
5061
|
IV: 9343737-9359587 |
| Transcript:C10C5.1c.1 | C10C5.1c.1 |
7323
|
IV: 9343737-9366454 |
| Transcript:C10C5.1e.1 | C10C5.1e.1 |
7323
|
IV: 9343737-9366454 |
| Transcript:C10C5.1g.1 | C10C5.1g.1 |
7329
|
IV: 9343737-9366454 |
| Transcript:C10C5.1h.1 | C10C5.1h.1 |
7215
|
IV: 9343737-9366454 |
Other
12 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:C10C5.1a | C10C5.1a |
7317
|
IV: 9343737-9343823 |
| CDS:C10C5.1f | C10C5.1f |
7209
|
IV: 9343737-9343823 |
| CDS:C10C5.1j | C10C5.1j |
5193
|
IV: 9343737-9343823 |
| CDS:C10C5.1k | C10C5.1k |
5061
|
IV: 9343737-9343823 |
| CDS:C10C5.1e | C10C5.1e |
7323
|
IV: 9343737-9343823 |
| CDS:C10C5.1g | C10C5.1g |
7329
|
IV: 9343737-9343823 |
| CDS:C10C5.1h | C10C5.1h |
7215
|
IV: 9343737-9343823 |
| CDS:C10C5.1b | C10C5.1b |
7203
|
IV: 9343737-9343823 |
| CDS:C10C5.1c | C10C5.1c |
7323
|
IV: 9343737-9343823 |
| CDS:C10C5.1d | C10C5.1d |
7209
|
IV: 9343737-9343823 |
| CDS:C10C5.1i | C10C5.1i |
5115
|
IV: 9343737-9343823 |
| CDS:C10C5.1l | C10C5.1l |
3117
|
IV: 9343737-9343823 |
338 Allele
| Public Name |
|---|
| gk964278 |
| gk964500 |
| gk962765 |
| gk962666 |
| gk958344 |
| tm10725 |
| tm10726 |
| WBVar02067842 |
| WBVar02021064 |
| WBVar02021065 |
| gk946490 |
| gk946489 |
| otn1873 |
| otn1874 |
| WBVar00573873 |
| WBVar00573870 |
| h17630 |
| h17279 |
| h4051 |
| h16967 |
| h16968 |
| h11705 |
| h16365 |
| WBVar01657287 |
| gk726407 |
| gk651882 |
| gk797115 |
| WBVar01581705 |
| gk403566 |
| gk863426 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00007505 | 9343359 | 9366511 | -1 |
4 Data Sets
| Name | URL |
|---|---|
| WormBaseAcedbConverter | |
| GO Annotation data set | |
| C. elegans genomic annotations (GFF3 Gene) | |
| Panther orthologue and paralogue predictions |
142 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 | |
| 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 |
| mRNAs that showed decreased expression in 1 cell mebryo comparing to in oocyte, according to RNAseq analysis. | Gaussian error propagation. As cutoff for the up-regulated genes authors used log2 fold change > 1 and P < 0.05 and as cutoff for the down-regulated genes authors used log2 fold change < -1 and P < 0.05. | WBPaper00045420:fertilization_downregulated_transcript | |
| 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 | |
| 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 | |
| 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 detected in germline isolated from day-1 adult hermaphrodite animals. | All three experiments have CPM >= 1. | WBPaper00067147:germline_expressed | |
| Proteins interacting with GST-FBXA-210(C-terminal) via IP-MS in young adult animals. Proteins shown here are enriched in GST | Fold change > 2 and p-value < 0.1 were defined as threshold for significance. | WBPaper00068277:FBXA-210(C-terminal)_interacting_YoungAdult | |
| 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 significantly decreased expression in N2 animals exposed to 0.1mM Paraquat from hatching to reaching adult stage. | DESeq2 version 1.22.2, p < 0.05 | WBPaper00064716:paraquat_downregulated | |
| Transcripts detected in body muscle nuclei according to a nuclear FACS-based strategy. | Cufflinks | WBPaper00065120:body-muscle-transcriptome | |
| Proteins that showed significantly decreased expression after 1-day-old wild type adults were exposed to cisplatin (300ug per mL) for 6 hours. | The differential expression analysis was performed in R. Differentially expressed proteins were identified by using a two-sided t-test on log-transformed data. | WBPaper00065373:Cisplatin_downregulated_WT | |
| Proteins that showed significantly decreased expression in 1-day-old sek-1(km4) adults comparing to in wild type animals, both with 6 hours of cisplatin treatment. | The differential expression analysis was performed in R. Differentially expressed proteins were identified by using a two-sided t-test on log-transformed data. | WBPaper00065373:sek-1(km4)_downregulated_cisplatin | |
| Genes that showed expression levels higher than the corresponding reference sample (L3/L4 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:dopaminergic-neurons_L3-L4-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:GABAergic-motor-neurons_L2-larva_expressed | |
| Transcripts that showed significantly altered expression at URX, AQR, and PQR neurons in camt-1(ok515) animals comparing to in wild type AX1888-1 strain. | RNA-seq data were mapped using PRAGUI - a Python 3-based pipeline for RNA-seq data analysis. | WBPaper00061902:camt-1(ok515)_regulated_URX-AQR-PQR | |
| Genes that showed expression levels higher than the corresponding reference sample (L3/L4 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:PVD-OLL-neurons_L3-L4-larva_expressed | |
| Transcripts that showed significantly increased expression in hda-2(ok1479) comparing to in N2 animals. | DESeq2 (version 1.28.1), FDR < 0.01, fold change > 2. | WBPaper00062159:hda-2(ok1479)_upregulated | |
| Transcripts that showed significantly altered expression in rnp-6(dh1127) animals comparing to in N2 when fed with heat killed E. coli OP50. | Differentially expressed genes (DEGs) (q-value <0.05) between different samples were identified using the stringtie version 1.3.0, followed by Cufflinks version 2.2. | WBPaper00059824:rnp-6(dh1127)_regulated_OP50 | |
| Transcripts that showed significantly altered expression in rnp-6(dh1127) animals comparing to in N2 when fed with live S. aureus. | Differentially expressed genes (DEGs) (q-value <0.05) between different samples were identified using the stringtie version 1.3.0, followed by Cufflinks version 2.2. | WBPaper00059824:rnp-6(dh1127)_regulated_S.aureus | |
| Genes that were not enriched in either spermatogenic fem-3(q96gf) nor oogenic fog-2(q71) gonads, according to RNAseq analysis. | To identify differentially expressed transcripts, authors used R/Bioconductor package DESeq. | WBPaper00045521:Gender_Neutral | |
| Proteins identified in extracellular vesicle. | N.A. | WBPaper00062669:extracellular-vesicle_protein | |
| Transcripts that showed significantly decreased expression in nhl-2(ok818) comparing to in N2 at 25C. | EdgeR, FDR < 0.05, fold change < 0.5. | WBPaper00055971:nhl-2(ok818)_25C_upregulated | |
| Maternal class (M): genes that are called present in at least one of the three PC6 replicates. | 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_M | |
| Transcripts that showed significantly increased expression after N2 animals were exposed to BL21 bacteria carrying pET28a-cry5B, comparing to animals exposed to BL21 control bacteria. | Differentially expressed genes were identified through fold change as well as P value calculated with t-test. The threshold set for up- and down-regulated genes was a fold change >= 2.0 and a P value <= 0.05. | WBPaper00065732:Cry5Ba_upregulated_N2 |
16 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr16012 | The strongest GFP signals that we identified came from the pharyngeal gland cells. Additionally, we visualized pezo- 1::GFP in a series of cells surrounding the muscle of the corpus and the isthmus (Albertson and Thomson, 1976). We also recognized the arcade cells as putative pezo-1-expressing cells, according to their morphology and location. We also observed many other anterior cells labeled with GFP; however, we cannot currently confirm if they represent neurons and/or amphids.By crossing pezo-1::GFP with a tph-1::DsRed marker-carrying strain, we were able to identify pezo-1 expression in the pha- ryngeal neurosecretory, motor, and sensory (propioceptive/ mechanosensory) neurons (NSML/R). In addition to the pharyngeal cells, we observed expression of pezo-1 in the ventral nerve cord neurons, according to their morphology and location, striated muscles, coelomocytes, spermatheca, vulval muscles, and various male neurons, including the ray neurons. | |||
| Expr16581 | We used a promoter immediately upstream of the start codon of pezo-1 isoform k to drive GFP expression. We saw labeling of pharyngeal isthmus muscles, pharyngeal glands, and cells with morphology and position consistent with arcade cells. We also saw GFP labeling in ventral neurons and in body wall muscles, where GFP colocalized with a Pmyo-3::mCherry body wall co-injection marker. | |||
| Expr16580 | We used a putative promoter 5 kb sequence immediately upstream of the start codon of pezo-1 isoforms i and j. GFP expression was mainly restricted to pharyngeal muscles and sensory neurons. In the pharynx, we saw GFP labeling of the pm3 muscle cells, the mc1 marginal cells in the corpus, a structure responsible for generating suction forces during the ingestion of suspended bacteria (Raizen et al. 2012), and in a neuron consistent in location and morphology with I4. A ventral cell located posterior to the terminal bulb and extending a process dorso-anteriorly toward the pharyngeal-intestinal valve (consistent with the excretory gland) was also labeled. Based on their location and characteristic extensive branching, we identified the anterior and posterior mechanoreceptors FLP and PVD (respectively) as also expressing GFP. Posteriorly, we tentatively identified a phasmid neuron consistent with the PHC neuron's morphology and location, as well as other cells associated with the uterus and anus, as expressing GFP. Unlike the other transcriptional constructs, GFP expression in these animals was visible as early as prezle-stage embryos. | |||
| Expr1033228 | Tiling arrays expression graphs | |||
| Expr16579 | Using a promoter immediately upstream of the start codon of the eight longest pezo-1 isoforms, we drove expression of GFP in several mesodermal tissues, including the body wall and pharyngeal muscles, pharyngeal glands and valve, and uterine and defecation tissues. Our findings are consistent with those described in a recent preprint by Millet et al. (2021). Based on their unique morphology and location, we identified GFP expression in pharyngeal muscles (pm3-8), pharyngeal glands (dg1, vg1s, vg2s), pharyngeal-intestinal valve (vpi) cells, AMsh, and AMso glial cells. We also tentatively identified pharyngeal neurons M1 and I4. Medially, we saw labeling of the HSN neuron, the vulval muscles, uterine muscles, and intestine. Posteriorly, we saw labeling in cells involved in defection. Based on their morphology and position, we tentatively identified these as rectD, K, F, B, U, and Y (N1⁄421). In addition to GFP-based transcriptional reporters, we used the CRISPR/Cas9-generated AG467 (integrated) strain which used mScarlet to tag the C terminus of PEZO-1 proteins. Imaging of AG467 (N 1⁄4 6) showed PEZO-1 proteins localized to the vicinity of the pharyngeal grinder, to the quadrants of the pharyngeal bulb occupied by the gland cells, and to the tip of the nose of the worm where the amphid sheath is located. We conclude that reporters upstream of long pezo-1 isoforms drive gene expression largely in muscles and other mesodermal tissues, although some neuronal expression was also seen. | |||
| Expr15070 | mScarlet::PEZO-1, and PEZO-1::mScarlet were widely expressed from embryonic stages through adulthood. Notably, PEZO-1 is strongly expressed in several tubular tissues, including the pharyngeal-intestinal and spermathecal-uterine valves. Under higher magnification, we observed PEZO-1 on the plasma membranes of oocytes and embryonic cells during a variety of embryonic stages, suggesting PEZO-1 is a transmembrane protein. PEZO-1 is expressed in multiple reproductive tissues, including the germline, somatic oviduct, and spermatheca. Higher magnification imaging of the spermatheca revealed expression of PEZO-1 on sperm membranes as well. Live imaging and detailed analysis of PEZO-1 expression patterns during reproduction revealed that GFP::PEZO-1 is expressed in sheath cells, sperm, both spermathecal valves and the spermathecal bag cells. | |||
| Expr1035227 | Tiling arrays expression graphs | |||
| Expr1144355 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| Expr1157169 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| Expr2014840 | 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). | |||
| Expr2043570 | 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 | |||
| Expr1027336 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
| Expr2033075 | 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). | |||
| Expr15071 | Under higher magnification, we observed PEZO-1 on the plasma membranes of oocytes and embryonic cells during a variety of embryonic stages, suggesting PEZO-1 is a transmembrane protein. | |||
| Expr15072 | Higher magnification imaging of the spermatheca revealed expression of PEZO-1 on sperm membranes as well. | |||
| Expr1015463 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 |
19 GO Annotation
| Annotation Extension | Qualifier |
|---|---|
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| enables | |
| enables | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| located_in | |
| located_in | |
| enables |
8 Homologues
| Type |
|---|
| orthologue |
| orthologue |
| orthologue |
| least diverged orthologue |
| least diverged orthologue |
| least diverged orthologue |
| orthologue |
| least diverged orthologue |
19 Ontology Annotations
| Annotation Extension | Qualifier |
|---|---|
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| enables | |
| enables | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| located_in | |
| located_in | |
| enables |
1 Upstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrIV_9366512..9366883 | 372 | IV: 9366512-9366883 | Caenorhabditis elegans |
