Genomics
1 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:C38C3.5.1 | C38C3.5.1 |
717
 |
V: 1475086-1479576 |
Other
1 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:C38C3.5 | C38C3.5 |
459
|
V: 1475139-1475141 |
103 Allele
| Public Name |
|---|
| WBVar01584584 |
| WBVar01584585 |
| WBVar01584582 |
| WBVar01584583 |
| gk963591 |
| gk963553 |
| gk964259 |
| gk963850 |
| r398 |
| gk963899 |
| gk963027 |
| gk964509 |
| s1309 |
| s1310 |
| s1307 |
| s1308 |
| s1331 |
| s1586 |
| s1983 |
| s1986 |
| su158 |
| WBVar01971039 |
| WBVar01971040 |
| gk964132 |
| WBVar00202889 |
| WBVar00202891 |
| WBVar00202890 |
| WBVar00202892 |
| WBVar02023035 |
| gk952929 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00006794 | 1475086 | 1479576 | 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_1479577..1482041 | 2465 | V: 1479577-1482041 | Caenorhabditis elegans |
169 Expression Clusters
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| oocyte proteins identified by two or more unique peptides during proteomics study. | In the pooled data set, 1453 C. elegans proteins were identified with a probability >= 0.9 according to ProteinProphet, of which 1165 proteins were identified by more than one unique peptide. | WBPaper00038289:oocyte_protein | |
| 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 |
| 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 | |
| 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 |
| Proteins interacting with NHR-49-GFP according to co-IP and LC-MS. | N.A. | WBPaper00064071:NHR-49_interacting | |
| 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 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 expressed in GABAergic neuron, according to PAT-Seq analysis using Punc-47-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:GABAergic-neuron_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 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 | |
| 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 expressed in NMDA neuron, according to PAT-Seq analysis using Pnmr-1-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:NMDA-neuron_expressed | |
| Genes up regulated in alg-1(gk214) comparing to in N2. | Differential expression was assessed using an empirical Bayes statistics using the eBayes function. | WBPaper00040823:alg-1(gk214)_upregulated | |
| Transcripts expressed in pharynx, according to PAT-Seq analysis using Pmyo-2-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:pharynx_expressed | |
| Transcripts expressed in seam cells, according to PAT-Seq analysis using Pgrd-10-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:seam_expressed | |
| 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 after 24 hours of induction of human beta Amyloid at young adult stage | A 2-fold change in expression level and a false discovery rate analog of p < 0.05. | WBPaper00064130:Beta-Amyloid_24h_upregulated_mRNA | |
| 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 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 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 detected in body muscle nuclei according to a nuclear FACS-based strategy. | Cufflinks | WBPaper00065120:body-muscle-transcriptome | |
| Transcripts that showed significantly increased expression in animals with germline-specific inx-14(RNAi) comparing to in aniamls fed with control vector, both exposed to PA14 infection. | DESeq2. Differentially-expressed genes (DEG) were identified based on two criteria: FDR (False discovery rateusing Benjamini-Hochberg adjusted p-values) < 0.01 and absolute value of log2(Fold Change) > 1. | WBPaper00066146:germline-inx-14(RNAi)_upregulated_PA14 | |
| 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 |
11 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Picture: Figure 5. | Expr4808 | Detailed immunolocalization studies revealed a preferential localization of UNC-87 to the center of the I-band region, whereas it was found to be absent from the distal edges of the thin filaments. Double staining of UNC-87 and actin showed a similar striated localization patterns for both proteins with no detectable signal at the dense bodies in the center of the striations. However, the band of UNC-87 was slightly narrower than that of actin, indicating that UNC-87 is absent from the distal portions of the thin filaments (near the pointed ends of the actin filaments). By contrast, CeTM has been shown previously to localize to the distal portion of the thin filaments, and, double staining of CeTM and UNC-87 indeed identified CeTM at the istal portion and UNC-87 at the central portion of the actin bands, albeit with some overlap. UNC-60B localized to the center of the actin bands between dense bodies, together with UNC-87. However, with the exception of this partial overlap, UNC-87 and UNC-60B mostly localized to different regions of the thin filaments. | ||
| Expr1864 | Expressed in muscle. | Both UNC-60B and CeTM became detectable in muscle cells at a very early stage of muscle development (~290 min), nearly at the same time. At the comma stage (290350 min), both UNC-60B and CeTM are diffusely localized in the cytoplasm and positions of nuclei are devoid of staining. After the 1.5-fold stage (~430 min), CeTM was gradually localized to a narrow region which represented myo-fibrils as determined by double staining with anti-actin antibody, whereas UNC-60B remained in the diffuse cytoplasm. This differential localization of UNC-60B and CeTM was maintained throughout the later embryonic development. In adult body wall muscle, CeTM and UNC-60B were also localized to different regions of thin filaments. Interestingly, the staining patterns of CeTM and actin were different. CeTM was localized in linear patterns, whereas actin was localized in ladder-like patterns in which the regions of dense bodies were devoid of staining. UNC-60B was stained as dotted lines between two lines of CeTM with little overlapping zones. Double staining of actin and UNC-60B showed that UNC-60B was localized to the central areas of the actin ladders between dense bodies. Double staining of vinculin, as a marker for dense bodies, and UNC-60B revealed that UNC-60B filled the gaps between dense bodies but was not colocalized with them. The shape of the UNC-60Bpositive dots was irregular, suggesting that association of UNC-60B with myofibrils is unstable and dynamic. | ||
| Picture: Fig. 2. The myoepithelial-sheath cells are smooth-muscle-like cells that surround oocytes at the proximal gonad. | Expr8233 | Immunofluorescent signals of UNC-60A was detected in the myoepithelial-sheath cells, which are also positive for MyoA myosin heavy chain, although the UNC-60A signals were much weaker than those in the oocytes (note that signals in the oocytes are saturated). Occasionally, authors found areas in which anti-UNC-60A antibody penetrated only into the myoepithelial sheath but not into the oocytes and were able to observe punctate localization of UNC-60A. These puncta localized along with filamentous actin. | ||
| Expr2036029 | 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). | |||
| Expr1032864 | Tiling arrays expression graphs | |||
| Expr2543 | In adult worms, UNC-60A was highly expressed in the intestine, germ cells in the distal gonad, oocytes and spermatheca but not in body wall muscle. UNC-60B was expressed in body wall muscle, vulva and spermatheca. Both ADF/cofilin isoforms were not detected in the smooth-muscle-like myoepithelial sheath cells. It was previously demonstrated that UNC-60B is not expressed in early embryos and become detectable from the comma to 1.5-fold stages (approximately 290 minutes after first cell division) only in the body wall muscle cells. UNC-60A was maternally expressed and present in most of embryonic cells throughout embryogenesis. In the later stages, staining of UNC-60A in the nerve ring became intense. | At the one-cell stage, UNC-60A was diffuse in the cytoplasm and localized to no particular structure. Actin was localized throughout the cortex as well as in the diffuse cytoplasm and assembled at the early cleavage site in the telophase of the first mitosis, whereas UNC-60A did not significantly accumulate in these structures. During progression of cytokinesis and after the two-cell stage, association of UNC-60A with the cortical regions, especially at the cell-cell boundaries became evident. In addition, UNC-60A was colocalized with actin to dot-like structures at the anterior cortex of each blastomere. These are believed to be remnants of cell division. UNC-60B is diffusely localized in the cytoplasm of the embryonic body wall muscle in the later stages. In adult worms, localization of the nuclei of the gonad by DAPI indicated that both UNC-60A and UNC-60B were mostly localized to the cytoplasm. Also, they were undetectable in sperm, which does not have an actomyosin system. | ||
| No GO_term assigned. | Expr1280 | UNC-60B was expressed in embryonic body wall muscle cells. Although weak maternal expression of UNC-60B was observed, its expression was remarkably upregulated in developing body wall muscle cells from the 1.5-fold stage. As myofibrils are assembled beneath the hypodermis in two- to 3-fold stages, UNC-60B was localized both in diffuse cytoplasm and striated myofibrils . | The spindle-shaped outline of the muscle cells were visible by the UNC-60B staining, but the nuclei were devoid of staining. The staining of UNC-60B in body wall muscle cells was diffuse and wider than the staining of actin. | |
| Expr11655 | At the time of invasion GFP::UNC-60A was present throughout the uterine tissue and at elevated levels in the anchor cell (1.35-fold greater levels versus neighboring uterine cells; n = 11 animals examined). GFP::UNC-60A was also more enriched at the invasive cell membrane (1.29-fold enrichment vs. 0.75-fold for neighboring uterine cells; n = 11 animals examined). | GFP::UNC-60A localized in punctate structures at the AC-basement membrane interface before invasion. To determine whether these structures were invadopodia, their localization was examined relative to F-actin and basement membrane breaching. A tight correlation between F-actin localization and UNC-60A enrichment at the AC-basement membrane interface was observed, as well as localization to the invadopodium that breached the basement membrane. Further, UNC-60A localization to the AC-basement membrane interface was dependent on the integrin INA-1/PAT-3, whose activity is required for invasion and promotes the localization of other invadopodia constituents. Thus, UNC-60A is a component of AC invadopodia. | ||
| Expr1146143 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| Expr2017893 | 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). | |||
| Expr1027412 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 |
22 GO Annotation
| Annotation Extension | Qualifier |
|---|---|
| involved_in | |
| involved_in | |
| enables | |
| enables | |
| enables | |
| enables | |
| 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 | |
| located_in | |
| involved_in | |
| involved_in |
19 Homologues
| Type |
|---|
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| least diverged orthologue |
| least diverged orthologue |
| least diverged orthologue |
| orthologue |
| orthologue |
| least diverged orthologue |
| orthologue |
| least diverged orthologue |
| least diverged orthologue |