Genomics
1 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:F08C6.7.1 | F08C6.7.1 |
1244
 |
X: 7570374-7573619 |
Other
1 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:F08C6.7 | F08C6.7 |
933
|
X: 7570640-7570972 |
65 Allele
| Public Name |
|---|
| gk964260 |
| gk963896 |
| gk963732 |
| gk963873 |
| gk963874 |
| gk964088 |
| gk964087 |
| WBVar01690170 |
| sf19 |
| su130 |
| tm601 |
| h18117 |
| gk285514 |
| WBVar01883641 |
| gk285513 |
| WBVar01883642 |
| gk285512 |
| WBVar01883643 |
| gk285511 |
| WBVar01883644 |
| gk285510 |
| gk285509 |
| gk285508 |
| WBVar01883639 |
| gk285507 |
| WBVar01883640 |
| gk956266 |
| gk285517 |
| gk285516 |
| WBVar01816004 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00006827 | 7570374 | 7573619 | -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_chrX_7569723..7570373 | 651 | X: 7569723-7570373 | Caenorhabditis elegans |
139 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 increased expression after animals were treated with 50uM Rifampicin and 250uM Allantoin from day 1 to day 3 adult hermaphradite. | DESeq2(v1.14.1), fold change > 2, p-value < 0.05 | WBPaper00055354:Rifampicin-Allantoin_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 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 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 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 | |
| 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 detected in germline isolated from day-1 adult hermaphrodite animals. | All three experiments have CPM >= 1. | WBPaper00067147:germline_expressed | |
| 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 | |
| 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 |
| Significantly upregulated genes from clk-1(qm30) microarrays using SAM algorithm with an FDR < 0.1 from adult-only chips. | SAM algorithm with an FDR < 0.1. | WBPaper00033065:clk-1(qm30)_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 that showed significantly decreased expression in N2 day 4 adults comparing to in N2 day 1 adult animals according to Illumina RNASeq. | DESeq fold change > 2, FDR < 0.05. | WBPaper00067499:Day4_vs_Day1_downregulated_Illumina | |
| Transcripts that showed significantly decreased expression in N2 day 5 adults comparing to in N2 day 1 adult animals according to Illumina RNASeq. | DESeq fold change > 2, FDR < 0.05. | WBPaper00067499:Day5_vs_Day1_downregulated_Illumina | |
| 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 N2 day 7 adults comparing to in N2 day 1 adult animals according to Illumina RNASeq. | DESeq fold change > 2, FDR < 0.05. | WBPaper00067499:Day7_vs_Day1_downregulated_Illumina | |
| 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 | |
| Expression Pattern Group C, enriched for genes involved in metabolic processes. | The significance (P 0.0001) of the relative age (time) was used to determine if a gene was differentially expressed between the three age (time) groups. The effect of this factor explaining gene expression differences was used to determine if the expression went up or down during the two age/time periods (t1 - t2 and t2 -t3). Authors used a permutation approach to determine the thresholds for the different mapping strategies. For each of the used models for eQTL mapping, authors used 23,000 permutations. For each permutation, authors randomly picked a spot; each spot could only be picked once. The gene expression and relative lifespan values were than randomly distributed over the RILs (and time points) and used for mapping. In this way, authors obtained a threshold for each of the explaining factors. For the single time points, authors used a FDR of 0.01 to adjust for multiple testing. The genome-wide threshold for this FDR is -log10 P = 3.8 for each of the three time points. For the combined models (t1 to t2 and t2 to t3), authors used a genome-wide threshold of -log10 P = 4, which resembles an FDR of 0.006, 0.001, and 0.006 for marker, age, and the interaction between marker and age, respectively. To determine the threshold for the single gene examples, authors used 1000 permutations as in the genome-wide threshold. The difference is that they use the gene under study in all of the permutations. The P-values for the gene specific thresholds were determined at FDR = 0.05. | WBPaper00036286:Pattern_C | |
| Transcripts depleted in purified oocyte P bodies comparing to in whole oocytes. | DESeq2, FDR < 0.05, fold change > 2. | WBPaper00065975:P-body_vs_oocyte_depleted | |
| 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 detected in body muscle nuclei according to a nuclear FACS-based strategy. | Cufflinks | WBPaper00065120:body-muscle-transcriptome |
13 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Clone: pUL#JRH/AA9 | Expr7497 | Many muscles from late embryo to adult - weaker expression in adult. Including: body wall muscles, some vulval, rectal, anterior head muscles. | ||
| Original chronogram file: chronogram.1079.xml | [F08C6.7:gfp] transcriptional fusion. | Chronogram67 | ||
| Original chronogram file: chronogram.1048.xml | [F08C6.7:gfp] transcriptional fusion. | Chronogram56 | ||
| Original chronogram file: chronogram.1017.xml | [F08C6.7:gfp] transcriptional fusion. | Chronogram22 | ||
| Expr2036060 | 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). | |||
| Expr1032891 | Tiling arrays expression graphs | |||
| Five independent lines in a wild-type background showed the same pattern of expression, although the level of expression varied somewhat between transgenic lines. Significantly, the same UNC-98::GFP was used to create two independent lines in an unc-98(su130) background, and both lines are fully rescued with respect to the muscle phenotype. In addition, the UNC-98::GFP showed that same pattern of expression and intracellular localization in both wild-type and unc-98(su130) backgrounds. | Expr2577 | Expression was first observed in the developing embryo at the 1.5- to 2-fold stage, also observed in larvae and adults. Expression observed in body wall muscle, anal depressor muscle and vulval muscles. | Expression was first observed in the developing embryo at the 1.5- to 2-fold stage, in which the UNC-98-GFP protein seemed localized to filamentous tracts, which generally follow myosin heavy chain A antibody staining, and therefore are interpreted to be located in myofibrils. Additionally, expression is seen in undefined puncta located along the filamentous tracts. In larvae and adults, expression was seen in body wall muscle, and in addition, anal depressor muscle and vulval muscles. Within adult body wall muscle, the UNC-98-GFP fusion localizes to dense bodies and M-lines. Within these muscle cells, prominent localization of the UNC-98-GFP in the nucleus was also seen. The UNC-98-GFP colocalizes with the DNA-binding dye DAPI. The signal is excluded from what seems to be the nucleolus and the UNC-98-GFP signal is discontinuous. This nuclear localization is consistent with the presence of the NLS sequences noted above. During development, the nuclear localization of UNC-98::GFP begins at the late L2 to early L3 larval stages. | |
| Expr1200172 | Data from the TransgeneOme project | |||
| Original chronogram file: chronogram.131.xml | [F08C6.7:gfp] transcriptional fusion. | Chronogram287 | ||
| Expr2017924 | 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). | |||
| Expr1015982 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
| Expr1147957 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| EU131 staining was undetectable in the muscle of each of the unc-98 mutants, consistent with the absence of the 37-kDa polypeptide on Western blots, and thus demonstrating the specificity of the antibodies for UNC-98 protein. | Expr2578 | In wild-type muscle fixed with methanol and paraformaldehyde on whole worms, or alternatively, ethanol or methanol on worm frozen sections, anti-UNC-98 staining was only found at the M-line; no staining was observed at the dense bodies or in nuclei. However, when frozen sections were fixed with n-heptane, staining of M-lines and, in addition, the muscle cell nuclei was observed. Thus, it would seem that there is indeed UNC-98 in the nucleus, but the epitopes detected by these antibodies are inactivated by the usual fixatives. UNC-98 antibodies were used to stain animals genotypically unc-98(su130) that were rescued with a transgenic array carrying the 8.1-kb unc-98rescuing fragment and rol-6 marker DNA. Because extrachromosomal arrays contain multiple expressed copies of an introduced gene, these unc-98-rescued animals are likely to express higher than wildtype levels of UNC-98. In these unc-98-rescued animals, anti-UNC-98 antibodies localize to all three structures labeled with UNC-98-GFP: M-lines, nuclei, and dense bodies. When used against wild-type embryos, these antibodies stain filamentous structures, presumably myofibrils, as early as the 1.5- to 2-fold stage. In wild-type adult animals fixed with methanol and paraformaldehyde, these antibodies stain the M-line region, colocalizing with UNC-89, a previously described component of the M-line region. |
25 GO Annotation
| Annotation Extension | Qualifier |
|---|---|
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| enables | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in |
50 Homologues
| Type |
|---|
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
25 Ontology Annotations
| Annotation Extension | Qualifier |
|---|---|
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| enables | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in |
