Genomics
2 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:F38A6.2a.1 | F38A6.2a.1 |
2743
 |
V: 20764971-20770161 |
| Transcript:F38A6.2b.1 | F38A6.2b.1 |
2667
|
V: 20765009-20769144 |
Other
2 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:F38A6.2a | F38A6.2a |
2676
|
V: 20765009-20765131 |
| CDS:F38A6.2b | F38A6.2b |
2667
|
V: 20765009-20765131 |
98 Allele
| Public Name |
|---|
| gk963271 |
| gk964176 |
| gk962705 |
| gk963489 |
| gk963304 |
| gk963809 |
| WBVar01756719 |
| WBVar01756720 |
| WBVar01756721 |
| WBVar01756722 |
| WBVar00073888 |
| WBVar00073887 |
| WBVar00073886 |
| WBVar00073885 |
| WBVar00073889 |
| WBVar00073891 |
| WBVar00073890 |
| WBVar00073895 |
| WBVar00073894 |
| WBVar00073893 |
| WBVar00073892 |
| WBVar01710529 |
| tm637 |
| tm638 |
| WBVar01544398 |
| WBVar01978796 |
| WBVar01978795 |
| WBVar01978794 |
| WBVar02026482 |
| ok347 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00001248 | 20764971 | 20770161 | -1 |
4 Data Sets
| Name | URL |
|---|---|
| WormBaseAcedbConverter | |
| GO Annotation data set | |
| C. elegans genomic annotations (GFF3 Gene) | |
| Panther orthologue and paralogue predictions |
1 Downstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrV_20763834..20764970 | 1137 | V: 20763834-20764970 | Caenorhabditis elegans |
157 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 | |
| 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 | |
| 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 decreased expression in AGP22 [nhr-49(nr2041)I;glp-1(e2141)III] comparing to in CF1903 [glp-1(e2144)III] at Day 2 adults. | Fold change > 2, p Value of < 0.05 and a false discovery rate (FDR) of < 0.05. | WBPaper00061530:nhr-49(e2144)_downregulated | |
| TGF- Dauer pathway adult transcriptional targets. Results obtained by comparing the microarray results of the dauer-constitutive mutants daf-7(e1372), daf-7(m62), and daf-1(m40) with dauer-defective mutants daf-3(mgDf90), daf-5(e1386), and daf-7(e1372);daf-3(mgDf90) double mutants at the permissive temperature, 20C, on the first day of adulthood. | SAM | WBPaper00031040:TGF-beta_adult_upregulated | |
| Osmotic stress | Transcripts that showed significantly altered expression with 500 mM salt (NaCl) vs 100 mM salt when food was present | DESeq(version 1.10.1), FDR < 0.05. | WBPaper00050726:OsmoticStress_regulated_Food |
| Osmotic stress | Transcripts that showed significantly altered expression with 500 mM salt (NaCl) vs 100 mM salt when no food was present | DESeq(version 1.10.1), FDR < 0.05. | WBPaper00050726:OsmoticStress_regulated_NoFood |
| Genes that showed expression levels higher than the corresponding reference sample (embryonic 24hr 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:bodywall-muscle_L1-larva_expressed | |
| 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 eft-2(RNAi) animals at zip-2(tm4248) background. | DESeq2, fold change > 2 and p-value < 0.01. | WBPaper00067953:eft-2(RNAi)_upregulated_zip-2(tm4248) | |
| 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 that showed significantly increased expression in eif-2alpha(RNAi) animals at zip-2(tm4248) background. | DESeq2, fold change > 2 and p-value < 0.01. | WBPaper00067953:eif-2alpha(RNAi)_upregulated_zip-2(tm4248) | |
| 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 | |
| Transcripts that showed significantly decreased expression at 11-days-post L4 adult N2 hermaphrodites comparing to 1-day-post L4 adult N2 hermaphrodites. | DESeq2, fold change > 2, FDR < 0.05 | WBPaper00065835:Day11_vs_Day1_downregulated | |
| 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 infection: Bacillus thuringiensis | mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 10 mix) vs BT407 6h), according to RNAseq. | Cuffdiff, ajusted p-value < 0.01. | WBPaper00046497:B.thuringiensis_0.1mix_downregulated_6h |
| Bacteria infection: Bacillus thuringiensis | mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 10 mix) vs BT407 12h), according to RNAseq. | Cuffdiff, ajusted p-value < 0.01. | WBPaper00046497:B.thuringiensis_0.1mix_downregulated_12h |
| 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 6h), according to RNAseq. | Cuffdiff, ajusted p-value < 0.01. | WBPaper00046497:B.thuringiensis_0.5mix_downregulated_6h |
| 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 | |
| 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 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 mrg-1(qa6200) comparing to in control animals in primordial germ cells (PGCs) at L1 larva stage. | DESeq2(v1.32.0), FDR < 0.05. | WBPaper00064315:mrg-1(qa6200)_upregulated_PGCs | |
| 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 | |
| Heat Shock: 35C 4 hours at L4 larva stage. | Transcripts that showed significantly decreased expression after L4 larva N2 animals were heat stressed at 35C for 4 hours | DESeq2 | WBPaper00057154:HeatShock_downregulated_mRNA |
| 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 |
6 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr1019699 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
| Picture: Fig 3, 4, 5. | Expr8965 | ELP-1::GFP was associated with the nine pairs of rays of the male tale. The relatively diffuse and broad band of fluorescence appears to originate from the hypodermal cells (hyp7) and one or more of the neuronal cells of the ray (RnA, RnB). In embryos, ELP-1::GFP expression first appeared during the comma stage. As the embryo matured into the 1-1.5 fold stage, the strongest expression was seen in the hypodermal cells, with only diffuse staining throughout the rest of the embryo. During larval development, expression of the fusion protein was progressively refined to muscle, neurons and epithelial cells. In the adult, ELP-1::GFP and ELP-1(truncated)::NLS::GFP were expressed in body wall muscle, spermatheca, vulval muscle, seam cells, the intestine, touch receptor neurons (TRNs) and inner labial 1 (IL1) neurons of the head. | At the subcellular level, ELP-1::GFP was associated with adhesion sites in both males and hermaphrodites. In the hermaphrodite body wall muscle, ELP-1::GFP was associated with the muscle arms that terminate in neuromuscular junctions. The ELP-1::GFP fluorescence is found throughout the muscle arm. In males, ELP-1::GFP associated with repeating focal attachment points in the sex-specific muscles of the worm. ELP-1 expression was prominent at the adhesion sites located at the sarcolemma. | |
| Expr1150555 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| Picture: Fig 6, 7, 8, 9. | Expr8966 | Affinity-purified antibodies against ELP-1 and the full-length ELP-1::GFP fusion protein localized to thin linear rows near the cell surface that were not quite parallel to the long axis of the muscle cell. At higher resolution there was a periodicity to these lines that approximated the distance between the dense body adhesion sites. The ELP-1::GFP fluorescence slightly overlaps the edges of the dense bodies but is not superimposable with the dense bodies at this angle. These results indicate that ELP-1 is unlikely to be a component of the dense bodies. Double-stained muscle cells with anti-ELP-1 antibodies and a monoclonal antibody MH25 against PAT-3 shows that integrin and ELP-1 have overlapping staining patterns at this level of resolution. Because of the relatively impenetrable cuticle that surrounds the nematode, these worms were frozen and cracked open prior to antibody staining. In areas lacking dense bodies, ELP-1::GFP was sometimes lost. However most of the ELP-1::GFP was retained in a linear pattern. These results indicate that the membrane and dense bodies can be separated from the ELP-1::GFP. Although the truncated construct and the full-length construct were expressed in the same cells and tissues, only the full length ELP-1::GFP construct localized to an elaborate array of fluorescent filaments. An obliquely striated fluorescent pattern emerges approximately 0.8 um apically from the base of the dense body. Deeper within the muscle body the filaments appear to separate from the linear track and branch out into the cytoplasm. ELP-1 was enriched in preparations of paclitaxel-stabilized microtubules in vitro. Paclitaxel-stabilized microtubules were prepared from a mixed-stage worm preparation and examined by means of Western blotting with an affinity-purified antisera against a bacterially expressed ELP-1 fusion protein. An ELP-1-reacting band co-purified with microtubules and migrated at ~100 kDa, a mass that corresponded to the Genefinder predictions for the larger ELP-1a polypeptide. Two smaller and less abundant proteins that cross-react with the ELP-1 antibodies also co-purified with microtubules. These may be isoforms generated by alternative splicing (i.e. ELP-1b) or proteolytic fragments of ELP-1a. This experiment and the one described above showed that ELP-1 is microtubule-associated both in situ and in vivo. To test the idea that the filaments decorated by ELP-1::GFP were microtubules, authors treated worms with the microtubule inhibitor, nocodazole. Worms were gently pressed between a slide and coverslip to extrude their intestines. This process was done in the presence of levamisole, an acetylcholine agonist, which was used to paralyze the worms for microscopy. The filaments in the extruded layer were stable for 30 minutes or more in the absence of nocodazole. The decorated filaments began to degrade within seconds and were entirely de-polymerized after two minutes in nocodazole. When the fluorescence disappeared the intestinal fragments noticeably flattened and the remnants of the worm contracted. This result indicates that ELP-1::GFP associates with microtubules in situ. | ||
| Expr2011287 | 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). | |||
| Expr2029523 | 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). |
10 GO Annotation
| Annotation Extension | Qualifier |
|---|---|
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| involved_in | |
| located_in | |
| enables | |
| located_in |
4 Homologues
| Type |
|---|
| least diverged orthologue |
| least diverged orthologue |
| least diverged orthologue |
| least diverged orthologue |
10 Ontology Annotations
| Annotation Extension | Qualifier |
|---|---|
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| involved_in | |
| located_in | |
| enables | |
| located_in |
1 Upstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrV_20770162..20772439 | 2278 | V: 20770162-20772439 | Caenorhabditis elegans |
