Genomics
1 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:C25F6.2.1 | C25F6.2.1 |
3780
 |
X: 5479700-5484941 |
Other
1 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:C25F6.2 | C25F6.2 |
2904
|
X: 5479761-5479782 |
34 RNAi Result
118 Allele
| Public Name |
|---|
| gk964260 |
| gk853194 |
| gk486535 |
| gk280617 |
| WBVar02063843 |
| WBVar02063844 |
| WBVar01758429 |
| WBVar01758430 |
| WBVar01758431 |
| WBVar00079119 |
| WBVar00079121 |
| WBVar00079120 |
| WBVar00079123 |
| WBVar00079122 |
| WBVar01549936 |
| WBVar01549934 |
| WBVar01549935 |
| WBVar01549933 |
| WBVar01830544 |
| gk636962 |
| gk587102 |
| gk710786 |
| tu1782 |
| WBVar01879444 |
| WBVar01879445 |
| WBVar01879446 |
| WBVar01879447 |
| WBVar01879440 |
| WBVar01879441 |
| WBVar01879442 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00001006 | 5479700 | 5484941 | 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_5484942..5485111 | 170 | X: 5484942-5485111 | Caenorhabditis elegans |
250 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 | |
| Transcripts that showed significantly increased expression in L1 neural cells comparing to in adult neural cells. | DESeq2 (v1.18.1) fold change > 2, P-adj<0.05, using BenjaminiHochberg correction. | WBPaper00060811:L1_vs_adult_upregulated_neural | |
| Transcripts expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons. | DESeq. False discovry rate (FDR) < 0.1. | WBPaper00048988:neuron_expressed | |
| 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: E.faecalis strain OG1RF | Transcripts that showed significantly increased expression after infection by E. faecalis OG1RF. | Ballgown was used to calculate differential expression of genes using FPKM data and to generate tables with fold change and P values. Genes were shortlisted with a cutoff of 2-fold change and P values of less than 0.05. | WBPaper00059754:E.faecalis_OG1RF_upregulated |
| 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 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 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 after animals were treated with 100uM Psora and 250uM Allantoin from day 1 to day 3 adult hermaphradite. | DESeq2(v1.14.1), fold change > 2, p-value < 0.05 | WBPaper00055354:Psora-Allantoin_upregulated | |
| Transcripts that showed significantly increased expression after animals were treated with 100uM Rapamycin and 50mM Metformin from day 1 to day 3 adult hermaphradite. | DESeq2(v1.14.1), fold change > 2, p-value < 0.05 | WBPaper00055354:Rapamycin-Metformin_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 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 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 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 expressed in NMDA neuron, according to PAT-Seq analysis using Pnmr-1-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:NMDA-neuron_expressed | |
| 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 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 | |
| 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 |
| 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 |
15 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr1030627 | Tiling arrays expression graphs | |||
| Picture: N.A. | Marker32 | adherens junction marker in epithelial cells | ||
| Expr10780 | In wild-type embryos, DLG-1 is well-distributed along the apical junctions of epithelia. | |||
| Expr1499 | DLG-1::GFP was first detected at the 350-cell stage in differentiating epithelial cells and neuroblasts. The neuronal expression was transient. After ventral enclosure, DLG-1::GFP was detected in the epidermis, pharynx and intestine, forming a continuous belt around epithelial cells at a subapical position, which persists throughout embryonic, larval and adult development. In adults, the DLG-1::GFP protein was also detected in epithelial cells contributing to the reproductive system: the vulva, uterus and spermatheca. | |||
| C25F6.2 is called dlg-1 in the article. | Expr804 | In wild-type embryos double labelling with mabMH27 reveals complete colocalisation of both antigens in adherens junctions of hypodermis, pharynx, and gut. In the early lima bean stage, both antigens first appear as a discontinuous punctate staining at the dorsal hypodermal cell borders. During more advanced morphogenesis (e.g., plum stage), they form a rectilinear intestine. | ||
| Expr15103 | The epidermis was the first epithelium to express dlg-1 mRNA. It was initially detected at the late 4E stage but with no detectableDLG-1 protein. The level of dlg-1 mRNA increased during the 8E stage and was maintained throughout the 16E and elongation stages (comma, 1.5-fold). DLG-1 protein was first observed during the late 8E stage, with puncta of protein visible on the membrane of nascent epidermal cells. These puncta began to coalesce at the early 16E stage and formed a continuous, circumferential junction by the mid-16E stage. The level of DLG-1 increased during the elongation stages (comma, 1.5-fold), as the cells changed shape to convert the embryo from a ball into a vermiform.The digestive tract began to express dlg-1 mRNA at the 8E stage, and, similar to the epidermis, the levels of RNA increased throughout the 8E and 16E stages. DLG-1 protein was first observed in midgut precursors at the early 16E stage, where puncta of protein appeared at the lateral surface and rapidly coalesced at the apical surface, in agreement with previous studies (Leung et al., 1999; Totong et al., 2007; Achilleos et al., 2010). By the mid-16E stage (20-40 min later), the puncta of DLG-1 had banded together to form cell junctions, which continued to expand and mature as the embryo elongated (comma, 1.5-fold stages). The RNA remained expressed in the intestine throughout all of these stages. In the foregut, DLG-1 protein was first detectable by the mid-16E stage, suggesting that translation of dlg-1 mRNA was delayed in this tissue by 20-40 min. We observed membrane-associated DLG-1 puncta on cell surfaces throughout the foregut at the 16E stage. These spots accumulated at the nascent apical surface by the bean stage, where they joined together to form connected junctions by the comma stage. The RNA remained expressed throughout these stages. The arcade cells are born during the mid-16E stage, starting 290 min after the first division (Sulston et al., 1983). The majority of these cells are anterior to the foregut primordium and express dlg-1 mRNA from birth. DLG-1 protein accumulated 100 min later in the arcades, after the epidermis and foregut had both formed epithelia and soon before the arcade cells became an epithelium (i.e., between the comma and 1.25-fold stage, 390-400 min after the first division; Portereiko and Mango, 2001; Portereiko et al., 2004). The presence of RNA but lack of protein was detectable by the 16E stage but was clearest at the comma stage, when the arcade cells clustered together as a group anterior to the foregut epithelium. Thus there was a delay in protein accumulation, suggesting that either the RNA was translationally repressed or protein was made but degraded immediately. | |||
| Expr15104 | The epidermis was the first epithelium to express dlg-1 mRNA. It was initially detected at the late 4E stage but with no detectableDLG-1 protein. The level of dlg-1 mRNA increased during the 8E stage and was maintained throughout the 16E and elongation stages (comma, 1.5-fold). DLG-1 protein was first observed during the late 8E stage, with puncta of protein visible on the membrane of nascent epidermal cells. These puncta began to coalesce at the early 16E stage and formed a continuous, circumferential junction by the mid-16E stage. The level of DLG-1 increased during the elongation stages (comma, 1.5-fold), as the cells changed shape to convert the embryo from a ball into a vermiform.The digestive tract began to express dlg-1 mRNA at the 8E stage, and, similar to the epidermis, the levels of RNA increased throughout the 8E and 16E stages. DLG-1 protein was first observed in midgut precursors at the early 16E stage, where puncta of protein appeared at the lateral surface and rapidly coalesced at the apical surface, in agreement with previous studies (Leung et al., 1999; Totong et al., 2007; Achilleos et al., 2010). By the mid-16E stage (20-40 min later), the puncta of DLG-1 had banded together to form cell junctions, which continued to expand and mature as the embryo elongated (comma, 1.5-fold stages). The RNA remained expressed in the intestine throughout all of these stages. In the foregut, DLG-1 protein was first detectable by the mid-16E stage, suggesting that translation of dlg-1 mRNA was delayed in this tissue by 20-40 min. We observed membrane-associated DLG-1 puncta on cell surfaces throughout the foregut at the 16E stage. These spots accumulated at the nascent apical surface by the bean stage, where they joined together to form connected junctions by the comma stage. The RNA remained expressed throughout these stages. The arcade cells are born during the mid-16E stage, starting 290 min after the first division (Sulston et al., 1983). The majority of these cells are anterior to the foregut primordium and express dlg-1 mRNA from birth. DLG-1 protein accumulated 100 min later in the arcades, after the epidermis and foregut had both formed epithelia and soon before the arcade cells became an epithelium (i.e., between the comma and 1.25-fold stage, 390-400 min after the first division; Portereiko and Mango, 2001; Portereiko et al., 2004). The presence of RNA but lack of protein was detectable by the 16E stage but was clearest at the comma stage, when the arcade cells clustered together as a group anterior to the foregut epithelium. Thus there was a delay in protein accumulation, suggesting that either the RNA was translationally repressed or protein was made but degraded immediately. | |||
| Expr1817 | The resulting fusion protein is situated at adherens junctions exclusively in epithelial cells of embryonic and adult epidermis, intestine, and pharynx. DLG-1::GFP is not expressed in neurons. | adherens junctions | ||
| Expr15128 | ||||
| Expr2010947 | 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). | |||
| Expr2876 | Staining of DLG-1 colocalizes with AJM-1 in the basal unit of the C. elegans apical junction. Similar results was obtained using an antibody against IFC-2, which normally anchor to desmosomes in vertebrates. The catenincadherin complex (alpha-cateninbeta-cateninE-cadherin; HMP-1HMP-2HMR-1) is found in immediate vicinity to DLG-1 in the apical unit of the C. elegans apical junction, but immuno-FLs seem to overlap partially. In contrast, anti-CRB-1 (Crumbs) and anti-DLG-1 staining is clearly separated, while CRB-1 and HMP-1 are found nearest to each other. The mabMH33 recognizes IFB-2 that localizes to the apical cytocortex of the gut epithelium. a-IFB-2 staining clearly overlaps subapically with CRB-1 and seems not to colocalize with DLG-1 in the basal unit of the C. elegans apical junction. | |||
| Expr16121 | We did not observe expression of endogenously tagged DLG-1::mNG protein in larval AQR (n 1⁄4 30). | |||
| Expr2029186 | 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). | |||
| Expr1145224 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| Expr1018466 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 |
37 GO Annotation
| Annotation Extension | Qualifier |
|---|---|
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| enables | |
| involved_in | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| located_in | |
| located_in | |
| involved_in | |
| located_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| located_in |
17 Homologues
| Type |
|---|
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| least diverged orthologue |
| least diverged orthologue |
| least diverged orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| least diverged orthologue |
37 Ontology Annotations
| Annotation Extension | Qualifier |
|---|---|
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| enables | |
| involved_in | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| located_in | |
| located_in | |
| involved_in | |
| located_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| located_in |
1 Upstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrX_5479046..5479699 | 654 | X: 5479046-5479699 | Caenorhabditis elegans |
